Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr10 129486693 

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32

Warning! 305 characters in sequence are not A, C, G, or T


File 354 of 444

Found at i:102587499 original size:16 final size:15

Alignment explanation

Indices: 102587468--102587507 Score: 53 Period size: 16 Copynumber: 2.6 Consensus size: 15 102587458 ATAAATAAAA * 102587468 TTTTAATTTTTAATT 1 TTTTATTTTTTAATT * 102587483 TTTTCATTTTTTCATT 1 TTTT-ATTTTTTAATT 102587499 TTTTATTTT 1 TTTTATTTT 102587508 AGAAATAATA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 15 9 0.41 16 13 0.59 ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78 Consensus pattern (15 bp): TTTTATTTTTTAATT Found at i:102587582 original size:18 final size:17 Alignment explanation

Indices: 102587521--102587580 Score: 61 Period size: 17 Copynumber: 3.6 Consensus size: 17 102587511 AATAATATAT * 102587521 AATAATTTTTAATTTAAA 1 AATAATTTTTAATTT-TA 102587539 AATAATTTTT-ATTTT- 1 AATAATTTTTAATTTTA ** * 102587554 TTTATTTTTTAATTTTA 1 AATAATTTTTAATTTTA 102587571 AATAATTTTT 1 AATAATTTTT 102587581 TAGAATTAAG Statistics Matches: 33, Mismatches: 7, Indels: 5 0.73 0.16 0.11 Matches are distributed among these distances: 15 7 0.21 16 5 0.15 17 11 0.33 18 10 0.30 ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63 Consensus pattern (17 bp): AATAATTTTTAATTTTA Found at i:102587609 original size:20 final size:18 Alignment explanation

Indices: 102587526--102587610 Score: 52 Period size: 18 Copynumber: 4.8 Consensus size: 18 102587516 TATATAATAA * * * 102587526 TTTTTAATTTAAAAATAA 1 TTTTTAATTTTAAATTAT * 102587544 TTTTT-ATTTT--TTTAT 1 TTTTTAATTTTAAATTAT * 102587559 TTTTTAATTTTAAATAAT 1 TTTTTAATTTTAAATTAT * * 102587577 TTTTTAGA-ATTAAGGTGTAT 1 TTTTTA-ATTTTAA-AT-TAT 102587597 TTTTTAATTTTAAA 1 TTTTTAATTTTAAA 102587611 AAATATATCT Statistics Matches: 49, Mismatches: 11, Indels: 13 0.67 0.15 0.18 Matches are distributed among these distances: 15 7 0.14 16 5 0.10 17 4 0.08 18 18 0.37 19 3 0.06 20 12 0.24 ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61 Consensus pattern (18 bp): TTTTTAATTTTAAATTAT Found at i:102594656 original size:13 final size:13 Alignment explanation

Indices: 102594638--102594677 Score: 71 Period size: 13 Copynumber: 3.1 Consensus size: 13 102594628 AGTTTGGCAA 102594638 TGCTTTTGAAAAG 1 TGCTTTTGAAAAG * 102594651 TGCTTTTGAGAAG 1 TGCTTTTGAAAAG 102594664 TGCTTTTGAAAAG 1 TGCTTTTGAAAAG 102594677 T 1 T 102594678 TTAGTTTAAA Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 13 25 1.00 ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40 Consensus pattern (13 bp): TGCTTTTGAAAAG Found at i:102606097 original size:24 final size:22 Alignment explanation

Indices: 102606069--102606143 Score: 64 Period size: 21 Copynumber: 3.2 Consensus size: 22 102606059 ACAAAAAAGA 102606069 TTTGTCTAAGTCATTTCGTTTCTT 1 TTTGTCTAAG-CATTTC-TTTCTT * * 102606093 TTTGTCCAAG--TTGCTTCTCTT 1 TTTGTCTAAGCATTTCTT-TCTT 102606114 TTTGTCTAACGCATTTCCTTTCTT 1 TTTGTCTAA-GCATTT-CTTTCTT 102606138 CTTTGT 1 -TTTGT 102606144 AAGTTTCAGG Statistics Matches: 41, Mismatches: 4, Indels: 11 0.73 0.07 0.20 Matches are distributed among these distances: 20 2 0.05 21 15 0.37 22 1 0.02 24 15 0.37 25 8 0.20 ACGTcount: A:0.11, C:0.21, G:0.12, T:0.56 Consensus pattern (22 bp): TTTGTCTAAGCATTTCTTTCTT Found at i:102608500 original size:17 final size:18 Alignment explanation

Indices: 102608457--102608519 Score: 85 Period size: 18 Copynumber: 3.6 Consensus size: 18 102608447 TTGATGATAC 102608457 CGATATTGATGATAGTGA 1 CGATATTGATGATAGTGA * 102608475 CGATATTGATGCTAGT-A 1 CGATATTGATGATAGTGA * 102608492 CGTTATTGATGATAGTGA 1 CGATATTGATGATAGTGA 102608510 C-ACTATTGAT 1 CGA-TATTGAT 102608520 CGTGACCTTG Statistics Matches: 39, Mismatches: 4, Indels: 4 0.83 0.09 0.09 Matches are distributed among these distances: 17 15 0.38 18 24 0.62 ACGTcount: A:0.30, C:0.10, G:0.24, T:0.37 Consensus pattern (18 bp): CGATATTGATGATAGTGA Found at i:102610266 original size:9 final size:9 Alignment explanation

Indices: 102610252--102610295 Score: 61 Period size: 9 Copynumber: 4.9 Consensus size: 9 102610242 CGTTCCATCA 102610252 TCCTTCTTT 1 TCCTTCTTT 102610261 TCCTTCTTT 1 TCCTTCTTT * 102610270 TCTTTCTTT 1 TCCTTCTTT * 102610279 TCTTTCTTT 1 TCCTTCTTT * 102610288 CCCTTCTT 1 TCCTTCTT 102610296 CTTTGACTCT Statistics Matches: 32, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 9 32 1.00 ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68 Consensus pattern (9 bp): TCCTTCTTT Found at i:102610543 original size:12 final size:12 Alignment explanation

Indices: 102610509--102610550 Score: 57 Period size: 12 Copynumber: 3.5 Consensus size: 12 102610499 GGCGATACCG 102610509 ATCTCTATCCCT 1 ATCTCTATCCCT * 102610521 ATCCCTATCCCT 1 ATCTCTATCCCT * 102610533 ATCTCTGTCCCT 1 ATCTCTATCCCT * 102610545 CTCTCT 1 ATCTCT 102610551 GTCACGGCCG Statistics Matches: 26, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 12 26 1.00 ACGTcount: A:0.12, C:0.45, G:0.02, T:0.40 Consensus pattern (12 bp): ATCTCTATCCCT Found at i:102637313 original size:25 final size:25 Alignment explanation

Indices: 102637285--102637335 Score: 102 Period size: 25 Copynumber: 2.0 Consensus size: 25 102637275 TGTGAGATTA 102637285 TAATATGTCTCATTCTGTATGCTCT 1 TAATATGTCTCATTCTGTATGCTCT 102637310 TAATATGTCTCATTCTGTATGCTCT 1 TAATATGTCTCATTCTGTATGCTCT 102637335 T 1 T 102637336 TGTGACCTAG Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 26 1.00 ACGTcount: A:0.20, C:0.20, G:0.12, T:0.49 Consensus pattern (25 bp): TAATATGTCTCATTCTGTATGCTCT Found at i:102638868 original size:6 final size:6 Alignment explanation

Indices: 102638857--102638911 Score: 74 Period size: 6 Copynumber: 9.2 Consensus size: 6 102638847 GTTTCCAAAC * * * * 102638857 ATGGAA ATGGAA ATAGAA ATGAAA ATGAAA ATGAAA ATGGAA ATGGAA 1 ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA 102638905 ATGGAA A 1 ATGGAA A 102638912 CCTGCAATAC Statistics Matches: 45, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 6 45 1.00 ACGTcount: A:0.58, C:0.00, G:0.25, T:0.16 Consensus pattern (6 bp): ATGGAA Found at i:102639109 original size:26 final size:27 Alignment explanation

Indices: 102639055--102639129 Score: 91 Period size: 26 Copynumber: 2.9 Consensus size: 27 102639045 AATTTTCTCG ** * 102639055 AAATTTTACTGAGGGTAAAATCAT-CA 1 AAATTTTACTGAGGGTAAAATTGTAAA 102639081 AAATTTTACTGAGGGTAAAATTGTAAA 1 AAATTTTACTGAGGGTAAAATTGTAAA ** 102639108 AAAAATTACT-AGGGTAAAATTG 1 AAATTTTACTGAGGGTAAAATTG 102639130 AGATGAAAAA Statistics Matches: 43, Mismatches: 5, Indels: 2 0.86 0.10 0.04 Matches are distributed among these distances: 26 34 0.79 27 9 0.21 ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31 Consensus pattern (27 bp): AAATTTTACTGAGGGTAAAATTGTAAA Found at i:102640777 original size:3 final size:3 Alignment explanation

Indices: 102640762--102640791 Score: 51 Period size: 3 Copynumber: 10.0 Consensus size: 3 102640752 GTGGTGATTT * 102640762 TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC 1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC 102640792 AAGTTTTGAC Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 3 25 1.00 ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70 Consensus pattern (3 bp): TTC Found at i:102641111 original size:43 final size:43 Alignment explanation

Indices: 102641050--102641247 Score: 238 Period size: 43 Copynumber: 4.6 Consensus size: 43 102641040 TTATCTAAAA * * * 102641050 AAACGCCGCTAAAGGTCATGACCTTTAATGGCGCTTTCCCCAC 1 AAACGCCGCTAAAAGTCATGACCTTTAACGGCGCTTTTCCCAC * * 102641093 AAACGCCGTTAAAAGTCATGACCTTTAACGGCGCTTTTGCCAC 1 AAACGCCGCTAAAAGTCATGACCTTTAACGGCGCTTTTCCCAC * * 102641136 AAATGCCGCTAAAAGTCATGACCTTTAGCGGCGCTTTTCCCAC 1 AAACGCCGCTAAAAGTCATGACCTTTAACGGCGCTTTTCCCAC * * * * 102641179 AAACGCAGCT-AAAGATCATGACCTTCAGCGACGCTTTTCCCAC 1 AAACGCCGCTAAAAG-TCATGACCTTTAACGGCGCTTTTCCCAC * * * 102641222 AAATGTCGCT-AAAGACCATGACCTTT 1 AAACGCCGCTAAAAG-TCATGACCTTT 102641248 GGAAAAAGTG Statistics Matches: 136, Mismatches: 18, Indels: 2 0.87 0.12 0.01 Matches are distributed among these distances: 42 4 0.03 43 132 0.97 ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24 Consensus pattern (43 bp): AAACGCCGCTAAAAGTCATGACCTTTAACGGCGCTTTTCCCAC Found at i:102641328 original size:74 final size:74 Alignment explanation

Indices: 102641186--102641328 Score: 162 Period size: 74 Copynumber: 1.9 Consensus size: 74 102641176 CACAAACGCA * * * * * ** * 102641186 GCTAAAGATCATGACCTTCAGCGACGCTTTTCCCACAAATGTCGCTAAAGACCATGACCTTTGGA 1 GCTAAAGATCATGACCTTCAGCAACACTTTTCCCAAAAACGTCGCTAAAGACCATAAAATTTGAA 102641251 AAAAGTGCC 66 AAAAGTGCC * * * * 102641260 GCTAAAGATCATGACCTTTAGTAACACTTTTCCCAAAAACG-CTGCTAAAGATCATAAAATTTTA 1 GCTAAAGATCATGACCTTCAGCAACACTTTTCCCAAAAACGTC-GCTAAAGACCATAAAATTTGA 102641324 AAAAA 65 AAAAA 102641329 TAAAATATTA Statistics Matches: 56, Mismatches: 12, Indels: 2 0.80 0.17 0.03 Matches are distributed among these distances: 73 1 0.02 74 55 0.98 ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25 Consensus pattern (74 bp): GCTAAAGATCATGACCTTCAGCAACACTTTTCCCAAAAACGTCGCTAAAGACCATAAAATTTGAA AAAAGTGCC Found at i:102641341 original size:10 final size:10 Alignment explanation

Indices: 102641328--102641353 Score: 52 Period size: 10 Copynumber: 2.6 Consensus size: 10 102641318 ATTTTAAAAA 102641328 ATAAAATATT 1 ATAAAATATT 102641338 ATAAAATATT 1 ATAAAATATT 102641348 ATAAAA 1 ATAAAA 102641354 GTCATGAAAA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 16 1.00 ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35 Consensus pattern (10 bp): ATAAAATATT Found at i:102645306 original size:3 final size:3 Alignment explanation

Indices: 102645300--102645340 Score: 82 Period size: 3 Copynumber: 13.7 Consensus size: 3 102645290 TTTTTCTCTT 102645300 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT 102645341 TACTAAAATG Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 38 1.00 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (3 bp): TTA Found at i:102645855 original size:14 final size:15 Alignment explanation

Indices: 102645816--102645846 Score: 62 Period size: 15 Copynumber: 2.1 Consensus size: 15 102645806 ACTATTTAAT 102645816 ATATAAATTAAAAAC 1 ATATAAATTAAAAAC 102645831 ATATAAATTAAAAAC 1 ATATAAATTAAAAAC 102645846 A 1 A 102645847 ATCACTTAAT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26 Consensus pattern (15 bp): ATATAAATTAAAAAC Found at i:102646138 original size:8 final size:7 Alignment explanation

Indices: 102646117--102646264 Score: 75 Period size: 7 Copynumber: 20.3 Consensus size: 7 102646107 CACACTAGTT 102646117 ACCCTAA 1 ACCCTAA 102646124 ACCCTAA 1 ACCCTAA 102646131 ACCCCT-A 1 A-CCCTAA * 102646138 ACCCTTA 1 ACCCTAA * 102646145 ACCCTTA 1 ACCCTAA * 102646152 ACCCTTA 1 ACCCTAA 102646159 ACCCTAAA 1 ACCCT-AA * 102646167 ACCCATAC 1 ACCC-TAA ** 102646175 ACATTTAA 1 AC-CCTAA * 102646183 ATCCTAA 1 ACCCTAA 102646190 ACCCTAA 1 ACCCTAA * 102646197 ACCCCATA 1 ACCCTA-A * 102646205 ACTCGTAA 1 AC-CCTAA 102646213 ACCCCT-A 1 A-CCCTAA * 102646220 ACTCTTAA 1 AC-CCTAA * 102646228 CCCCTAA 1 ACCCTAA 102646235 ACCCTAA 1 ACCCTAA * * 102646242 GCCATAA 1 ACCCTAA * * 102646249 AACATAA 1 ACCCTAA 102646256 ACCCTAA 1 ACCCTAA 102646263 AC 1 AC 102646265 TTCTTCCCCT Statistics Matches: 108, Mismatches: 23, Indels: 20 0.72 0.15 0.13 Matches are distributed among these distances: 6 5 0.05 7 75 0.69 8 24 0.22 9 4 0.04 ACGTcount: A:0.40, C:0.39, G:0.01, T:0.20 Consensus pattern (7 bp): ACCCTAA Found at i:102646140 original size:14 final size:14 Alignment explanation

Indices: 102646117--102646241 Score: 58 Period size: 15 Copynumber: 8.5 Consensus size: 14 102646107 CACACTAGTT 102646117 ACCCTAAA-CCCTAA 1 ACCCTAAACCCCT-A * 102646131 ACCCCT-AACCCTTA 1 A-CCCTAAACCCCTA * * 102646145 ACCCTTAACCCTTA 1 ACCCTAAACCCCTA * 102646159 ACCCTAAAACCCATA 1 ACCCT-AAACCCCTA ** * 102646174 CACATTTAAA-TCCTAA 1 -AC-CCTAAACCCCT-A 102646190 ACCCTAAACCCCATA 1 ACCCTAAACCCC-TA * 102646205 ACTCGTAAACCCCTA 1 AC-CCTAAACCCCTA * * 102646220 ACTCTTAACCCCTAA 1 ACCCTAAACCCCT-A 102646235 ACCCTAA 1 ACCCTAA 102646242 GCCATAAAAC Statistics Matches: 84, Mismatches: 16, Indels: 21 0.69 0.13 0.17 Matches are distributed among these distances: 13 4 0.05 14 30 0.36 15 33 0.39 16 16 0.19 17 1 0.01 ACGTcount: A:0.38, C:0.41, G:0.01, T:0.21 Consensus pattern (14 bp): ACCCTAAACCCCTA Found at i:102646597 original size:15 final size:15 Alignment explanation

Indices: 102646573--102646624 Score: 61 Period size: 15 Copynumber: 3.5 Consensus size: 15 102646563 TATACCCATG * 102646573 ACCATTAAACCTTAA 1 ACCATAAAACCTTAA * 102646588 ACCATAAAACCCTAA 1 ACCATAAAACCTTAA * 102646603 ACCAT-AGACCTTAA 1 ACCATAAAACCTTAA * 102646617 ACCTTAAA 1 ACCATAAA 102646625 TATTAAACCC Statistics Matches: 30, Mismatches: 6, Indels: 2 0.79 0.16 0.05 Matches are distributed among these distances: 14 11 0.37 15 19 0.63 ACGTcount: A:0.48, C:0.29, G:0.02, T:0.21 Consensus pattern (15 bp): ACCATAAAACCTTAA Found at i:102646624 original size:36 final size:35 Alignment explanation

Indices: 102646568--102646640 Score: 103 Period size: 36 Copynumber: 2.1 Consensus size: 35 102646558 TACTATATAC 102646568 CCATGACCATTAAACCTTAAACCATAAAACCCTAAA 1 CCATGACCATTAAACCTTAAA-CATAAAACCCTAAA * * 102646604 CCATAGACC-TTAAACCTTAAATATTAAACCCTAAA 1 CCAT-GACCATTAAACCTTAAACATAAAACCCTAAA 102646639 CC 1 CC 102646641 CCAAAATAAA Statistics Matches: 34, Mismatches: 2, Indels: 3 0.87 0.05 0.08 Matches are distributed among these distances: 35 14 0.41 36 16 0.47 37 4 0.12 ACGTcount: A:0.45, C:0.30, G:0.03, T:0.22 Consensus pattern (35 bp): CCATGACCATTAAACCTTAAACATAAAACCCTAAA Found at i:102646641 original size:7 final size:7 Alignment explanation

Indices: 102646577--102646640 Score: 56 Period size: 7 Copynumber: 9.0 Consensus size: 7 102646567 CCCATGACCA 102646577 TTAAACC 1 TTAAACC 102646584 TTAAACC 1 TTAAACC * 102646591 ATAAAACC 1 -TTAAACC * 102646599 CTAAACC 1 TTAAACC * * 102646606 ATAGACC 1 TTAAACC 102646613 TTAAACC 1 TTAAACC ** 102646620 TTAAATA 1 TTAAACC 102646627 TTAAACC 1 TTAAACC * 102646634 CTAAACC 1 TTAAACC 102646641 CCAAAATAAA Statistics Matches: 44, Mismatches: 12, Indels: 2 0.76 0.21 0.03 Matches are distributed among these distances: 7 38 0.86 8 6 0.14 ACGTcount: A:0.47, C:0.28, G:0.02, T:0.23 Consensus pattern (7 bp): TTAAACC Found at i:102646810 original size:38 final size:39 Alignment explanation

Indices: 102646763--102646846 Score: 134 Period size: 38 Copynumber: 2.2 Consensus size: 39 102646753 TGTTTAAGGT * * * 102646763 TTTAGGGGTTATAGTTTAGTGTTTATGGTT-TTTTAGGG 1 TTTAGGGGTTATAGATTAGTGTTTATGATTCTTTGAGGG 102646801 TTTAGGGGTTATAGATTAGTGTTTATGATTCTTTGAGGG 1 TTTAGGGGTTATAGATTAGTGTTTATGATTCTTTGAGGG 102646840 TTTAGGG 1 TTTAGGG 102646847 TTTTAGGGGT Statistics Matches: 42, Mismatches: 3, Indels: 1 0.91 0.07 0.02 Matches are distributed among these distances: 38 28 0.67 39 14 0.33 ACGTcount: A:0.18, C:0.01, G:0.32, T:0.49 Consensus pattern (39 bp): TTTAGGGGTTATAGATTAGTGTTTATGATTCTTTGAGGG Found at i:102646939 original size:41 final size:40 Alignment explanation

Indices: 102646865--102646951 Score: 106 Period size: 41 Copynumber: 2.1 Consensus size: 40 102646855 GTTATATAAC * * 102646865 TTTTTGCGGCGTTTTGACCACAAACGTCACTATTGTTCTGG 1 TTTTTGCGGCGTTTTGACCAAAAACGTCACTATTGCTCT-G * 102646906 TTTTTAGCGGCGTTTT-ACCAAAAACG-CTGCTATTGCTCTG 1 TTTTT-GCGGCGTTTTGACCAAAAACGTC-ACTATTGCTCTG 102646946 TTTTTG 1 TTTTTG 102646952 TTAAGACGCC Statistics Matches: 41, Mismatches: 3, Indels: 6 0.82 0.06 0.12 Matches are distributed among these distances: 39 1 0.02 40 7 0.17 41 23 0.56 42 10 0.24 ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41 Consensus pattern (40 bp): TTTTTGCGGCGTTTTGACCAAAAACGTCACTATTGCTCTG Found at i:102650848 original size:6 final size:6 Alignment explanation

Indices: 102650832--102650877 Score: 76 Period size: 6 Copynumber: 7.7 Consensus size: 6 102650822 ATTTTAAATT 102650832 TTTAGTA TTTATA TTTATA TTTATA TTTATA TTTATA TTTA-A TTTA 1 TTTA-TA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTA 102650878 GTCTTAATTT Statistics Matches: 39, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 5 5 0.13 6 30 0.77 7 4 0.10 ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65 Consensus pattern (6 bp): TTTATA Found at i:102652502 original size:38 final size:37 Alignment explanation

Indices: 102652429--102652503 Score: 89 Period size: 38 Copynumber: 2.0 Consensus size: 37 102652419 GTTATTAAAT * ** 102652429 TTTTATAAAAAATAAAAAATATTTAAAATTTAGAGAA 1 TTTTATAAAAAATAAAAAATATATAAAATAAAGAGAA * 102652466 TTTTATAAAAATCGTAAAAAA-ATATAAAATAAAGAGAA 1 TTTTATAAAAA--ATAAAAAATATATAAAATAAAGAGAA 102652504 ATATAGAAAA Statistics Matches: 32, Mismatches: 4, Indels: 3 0.82 0.10 0.08 Matches are distributed among these distances: 37 11 0.34 38 14 0.44 39 7 0.22 ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31 Consensus pattern (37 bp): TTTTATAAAAAATAAAAAATATATAAAATAAAGAGAA Found at i:102652786 original size:9 final size:9 Alignment explanation

Indices: 102652772--102652897 Score: 96 Period size: 9 Copynumber: 13.4 Consensus size: 9 102652762 TTTTGATGCA * 102652772 TTTTATAGT 1 TTTTATAAT * 102652781 TTTTATGAT 1 TTTTATAAT * 102652790 TTTTATAAAA 1 TTTTAT-AAT 102652800 TTTTATAAT 1 TTTTATAAT 102652809 TTTTACT-AT 1 TTTTA-TAAT 102652818 TTTTATAAT 1 TTTTATAAT 102652827 TTTTAATAATT 1 TTTT-ATAA-T * 102652838 TTTTATTAAAA 1 TTTTA-T-AAT * 102652849 TTTAATAATT 1 TTTTATAA-T 102652859 TTTTATAAT 1 TTTTATAAT * * 102652868 TTTAATTGAT 1 TTTTA-TAAT 102652878 TTTTAT--T 1 TTTTATAAT 102652885 TTTTATAAT 1 TTTTATAAT 102652894 TTTT 1 TTTT 102652898 TTTGCCACAT Statistics Matches: 94, Mismatches: 12, Indels: 22 0.73 0.09 0.17 Matches are distributed among these distances: 7 7 0.07 8 1 0.01 9 46 0.49 10 28 0.30 11 10 0.11 12 2 0.02 ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65 Consensus pattern (9 bp): TTTTATAAT Found at i:102652793 original size:18 final size:17 Alignment explanation

Indices: 102652772--102652897 Score: 69 Period size: 19 Copynumber: 6.8 Consensus size: 17 102652762 TTTTGATGCA * 102652772 TTTTATAGTTTTTATGAT 1 TTTTATAATTTTTAT-AT * 102652790 TTTTATAAAATTTTATAAT 1 TTTTAT-AATTTTTAT-AT 102652809 TTTTACT-ATTTTTATAAT 1 TTTTA-TAATTTTTAT-AT 102652827 TTTTAATAATTTTT-TAT 1 TTTT-ATAATTTTTATAT 102652844 TAAAATTTAATAATTTTTTATAAT 1 T----TTT-ATAA-TTTTTAT-AT * * 102652868 TTTAATTGATTTTTAT-T 1 TTTTA-TAATTTTTATAT 102652885 TTTTATAATTTTT 1 TTTTATAATTTTT 102652898 TTTGCCACAT Statistics Matches: 88, Mismatches: 8, Indels: 26 0.72 0.07 0.21 Matches are distributed among these distances: 16 7 0.08 17 8 0.09 18 22 0.25 19 29 0.33 20 5 0.06 21 8 0.09 22 5 0.06 23 1 0.01 24 3 0.03 ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65 Consensus pattern (17 bp): TTTTATAATTTTTATAT Found at i:102652802 original size:28 final size:28 Alignment explanation

Indices: 102652771--102652840 Score: 90 Period size: 28 Copynumber: 2.5 Consensus size: 28 102652761 TTTTTGATGC * 102652771 ATTTTATAGTTTTTA-TGATTTTTATAAA 1 ATTTTATAATTTTTACT-ATTTTTATAAA 102652799 ATTTTATAATTTTTACTATTTTTAT-AA 1 ATTTTATAATTTTTACTATTTTTATAAA * 102652826 TTTTTAATAATTTTT 1 ATTTT-ATAATTTTT 102652841 TATTAAAATT Statistics Matches: 38, Mismatches: 2, Indels: 4 0.86 0.05 0.09 Matches are distributed among these distances: 27 6 0.16 28 31 0.82 29 1 0.03 ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64 Consensus pattern (28 bp): ATTTTATAATTTTTACTATTTTTATAAA Found at i:102652866 original size:10 final size:10 Alignment explanation

Indices: 102652780--102652870 Score: 73 Period size: 10 Copynumber: 9.3 Consensus size: 10 102652770 CATTTTATAG * 102652780 TTTTTATGA- 1 TTTTTATAAT * 102652789 TTTTTATAAA 1 TTTTTATAAT * 102652799 ATTTTATAA- 1 TTTTTATAAT 102652808 TTTTTACT-A- 1 TTTTTA-TAAT 102652817 TTTTTATAAT 1 TTTTTATAAT * 102652827 TTTTAATAAT 1 TTTTTATAAT * 102652837 TTTTTATTAAA 1 TTTTTA-TAAT * * 102652848 ATTTAATAAT 1 TTTTTATAAT 102652858 TTTTTATAAT 1 TTTTTATAAT 102652868 TTT 1 TTT 102652871 AATTGATTTT Statistics Matches: 66, Mismatches: 11, Indels: 9 0.77 0.13 0.10 Matches are distributed among these distances: 8 1 0.02 9 21 0.32 10 37 0.56 11 7 0.11 ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64 Consensus pattern (10 bp): TTTTTATAAT Found at i:102653719 original size:29 final size:29 Alignment explanation

Indices: 102653687--102653744 Score: 73 Period size: 29 Copynumber: 2.0 Consensus size: 29 102653677 CTGGTTTTTC * * 102653687 AAGTTAGTTAGTCTGTTAG-TAGTTAGCTA 1 AAGTCAGTTAGT-TGTTAGCTAGGTAGCTA * 102653716 AAGTCAGTTCGTTGTTAGCTAGGTAGCTA 1 AAGTCAGTTAGTTGTTAGCTAGGTAGCTA 102653745 TTACTCTATT Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 28 6 0.24 29 19 0.76 ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38 Consensus pattern (29 bp): AAGTCAGTTAGTTGTTAGCTAGGTAGCTA Found at i:102661867 original size:30 final size:30 Alignment explanation

Indices: 102661831--102661899 Score: 79 Period size: 30 Copynumber: 2.3 Consensus size: 30 102661821 GTCACAATTA * 102661831 ACCA-TTTCTCGTTATAGACGTAAC-GAGGCT 1 ACCATTTTCT-GTTAGAGACGTAACAGA-GCT * * 102661861 ACCATTTTCTGTTAGATACTTAACAGAGCT 1 ACCATTTTCTGTTAGAGACGTAACAGAGCT 102661891 ACCATTTTC 1 ACCATTTTC 102661900 CATCCCCTTA Statistics Matches: 34, Mismatches: 3, Indels: 4 0.83 0.07 0.10 Matches are distributed among these distances: 30 27 0.79 31 7 0.21 ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35 Consensus pattern (30 bp): ACCATTTTCTGTTAGAGACGTAACAGAGCT Found at i:102663187 original size:48 final size:47 Alignment explanation

Indices: 102663092--102663196 Score: 126 Period size: 48 Copynumber: 2.3 Consensus size: 47 102663082 AAGGGACAAT * * 102663092 GGGGGAGAGGGAAAGAATAAGAGTAGGAGGAGGGATGGTAGATAAGA 1 GGGGGAGAGGGAAAGAATAAGAGAAGGAGGAGGGATGGTAGAGAAGA * * * 102663139 GGGGGAGAGGGAGAGAGAATCAGAGAAGG-GGAGGGATGGTGGGGAAGA 1 GGGGGAGAGGGA-A-AGAATAAGAGAAGGAGGAGGGATGGTAGAGAAGA 102663187 --GGGAGAGGGA 1 GGGGGAGAGGGA 102663197 TGGGAGAGCA Statistics Matches: 51, Mismatches: 5, Indels: 5 0.84 0.08 0.08 Matches are distributed among these distances: 46 10 0.20 47 12 0.24 48 17 0.33 49 12 0.24 ACGTcount: A:0.36, C:0.01, G:0.55, T:0.08 Consensus pattern (47 bp): GGGGGAGAGGGAAAGAATAAGAGAAGGAGGAGGGATGGTAGAGAAGA Found at i:102663288 original size:30 final size:30 Alignment explanation

Indices: 102663217--102663288 Score: 90 Period size: 30 Copynumber: 2.4 Consensus size: 30 102663207 GTGATAGGGG * * 102663217 ATGGAAAATGGCAACTTCGTTAAGTATCTA 1 ATGGAAAATGGTAACTCCGTTAAGTATCTA * * * * 102663247 ATGGAAAATGGTAGCTCCGTTACGTTTGTA 1 ATGGAAAATGGTAACTCCGTTAAGTATCTA 102663277 ATGGAAAATGGT 1 ATGGAAAATGGT 102663289 TGTGGTGACT Statistics Matches: 36, Mismatches: 6, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 30 36 1.00 ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31 Consensus pattern (30 bp): ATGGAAAATGGTAACTCCGTTAAGTATCTA Found at i:102674257 original size:28 final size:28 Alignment explanation

Indices: 102674226--102674282 Score: 64 Period size: 28 Copynumber: 2.0 Consensus size: 28 102674216 AATTTTGATG * 102674226 AAATCAGCTATTTG-GGG-CTAATTTGTGA 1 AAATCAG-T-TTTGAGGGACTAAATTGTGA * 102674254 AAATGAGTTTTGAGGGACTAAATTGTGA 1 AAATCAGTTTTGAGGGACTAAATTGTGA 102674282 A 1 A 102674283 TTAAATGTGT Statistics Matches: 25, Mismatches: 2, Indels: 4 0.81 0.06 0.13 Matches are distributed among these distances: 26 4 0.16 27 4 0.16 28 17 0.68 ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33 Consensus pattern (28 bp): AAATCAGTTTTGAGGGACTAAATTGTGA Found at i:102676880 original size:27 final size:26 Alignment explanation

Indices: 102676831--102676989 Score: 176 Period size: 27 Copynumber: 5.9 Consensus size: 26 102676821 AGGAAACGTC * * 102676831 CTGGTGGCTATGCTACAATTATCTGAT 1 CTGGTGGCTCTGCCACAA-TATCTGAT 102676858 CTGGTGGCTCTGCCACATATATCTG-T 1 CTGGTGGCTCTGCCACA-ATATCTGAT * 102676884 CCTGGTGGCTATGCCACAATTATCTGAT 1 -CTGGTGGCTCTGCCACAA-TATCTGAT * 102676912 CTGGTGGCTCTGCCACATATATCTGTT 1 CTGGTGGCTCTGCCACA-ATATCTGAT * * 102676939 CTGCTGGCTCTACCACAATATCTGTAT 1 CTGGTGGCTCTGCCACAATATCTG-AT * * * 102676966 CTGGTGACTCCGTCACAATATCTG 1 CTGGTGGCTCTGCCACAATATCTG 102676990 GCAGCCTCAC Statistics Matches: 113, Mismatches: 13, Indels: 12 0.82 0.09 0.09 Matches are distributed among these distances: 26 9 0.08 27 101 0.89 28 3 0.03 ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34 Consensus pattern (26 bp): CTGGTGGCTCTGCCACAATATCTGAT Found at i:102676910 original size:54 final size:54 Alignment explanation

Indices: 102676828--102676989 Score: 229 Period size: 54 Copynumber: 3.0 Consensus size: 54 102676818 TGGAGGAAAC * 102676828 GTCCTGGTGGCTATGCTACAATTATCTGATCTGGTGGCTCTGCCACATATATCT 1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT 102676882 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT 1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT * * * * * * * 102676936 GTTCTGCTGGCTCTACCACAA-TATCTGTATCTGGTGACTCCGTCACA-ATATCT 1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTGGCTCTGCCACATATATCT 102676989 G 1 G 102676990 GCAGCCTCAC Statistics Matches: 99, Mismatches: 8, Indels: 3 0.90 0.07 0.03 Matches are distributed among these distances: 53 13 0.13 54 86 0.87 ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34 Consensus pattern (54 bp): GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT Found at i:102684456 original size:27 final size:27 Alignment explanation

Indices: 102684420--102684483 Score: 69 Period size: 28 Copynumber: 2.3 Consensus size: 27 102684410 GTCTTTGAAT 102684420 TTTGATGAAATGAGCTATTTG-GGG-CTAA 1 TTTG-TGAAATGAG-T-TTTGAGGGACTAA 102684448 TTTGTGAAAATGAGTTTTGAGGGACTAA 1 TTTGTG-AAATGAGTTTTGAGGGACTAA * 102684476 ATTGTGAA 1 TTTGTGAA 102684484 TTAAATATGT Statistics Matches: 32, Mismatches: 1, Indels: 7 0.80 0.03 0.17 Matches are distributed among these distances: 26 4 0.12 27 8 0.25 28 20 0.62 ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36 Consensus pattern (27 bp): TTTGTGAAATGAGTTTTGAGGGACTAA Found at i:102684458 original size:28 final size:28 Alignment explanation

Indices: 102684427--102684483 Score: 73 Period size: 28 Copynumber: 2.0 Consensus size: 28 102684417 AATTTTGATG * 102684427 AAATGAGCTATTTG-GGG-CTAATTTGTGA 1 AAATGAG-T-TTTGAGGGACTAAATTGTGA 102684455 AAATGAGTTTTGAGGGACTAAATTGTGA 1 AAATGAGTTTTGAGGGACTAAATTGTGA 102684483 A 1 A 102684484 TTAAATATGT Statistics Matches: 26, Mismatches: 1, Indels: 4 0.84 0.03 0.13 Matches are distributed among these distances: 26 4 0.15 27 4 0.15 28 18 0.69 ACGTcount: A:0.33, C:0.05, G:0.28, T:0.33 Consensus pattern (28 bp): AAATGAGTTTTGAGGGACTAAATTGTGA Found at i:102698280 original size:26 final size:26 Alignment explanation

Indices: 102698251--102698392 Score: 100 Period size: 26 Copynumber: 5.7 Consensus size: 26 102698241 CTTATTAGTG * 102698251 TCCCGATATATGGCTCTTCGTGAGCT 1 TCCCGATATATGGCTCTCCGTGAGCT * ** 102698277 TCCCGTTGAT-TGGCTCTTTGTGAGCT 1 TCCCGAT-ATATGGCTCTCCGTGAGCT ** 102698303 TCTTGAT-TAATGGCTCTCCG-GAGCT 1 TCCCGATAT-ATGGCTCTCCGTGAGCT * * * * 102698328 TCCCAATAT-TGGCT-TGCTTGAACT 1 TCCCGATATATGGCTCTCCGTGAGCT * * 102698352 TCCCAATATATGGCTATCCG-GAGCT 1 TCCCGATATATGGCTCTCCGTGAGCT * 102698377 TCCCGTTA-ATGGCTCT 1 TCCCGATATATGGCTCT 102698393 ATGGAGCTAC Statistics Matches: 90, Mismatches: 19, Indels: 16 0.72 0.15 0.13 Matches are distributed among these distances: 23 2 0.02 24 26 0.29 25 24 0.27 26 36 0.40 27 2 0.02 ACGTcount: A:0.16, C:0.26, G:0.22, T:0.36 Consensus pattern (26 bp): TCCCGATATATGGCTCTCCGTGAGCT Found at i:102698378 original size:25 final size:24 Alignment explanation

Indices: 102698312--102698380 Score: 77 Period size: 24 Copynumber: 2.8 Consensus size: 24 102698302 TTCTTGATTA 102698312 ATGGCTCTCCGGAGCTTCCCAATAT 1 ATGGCT-TCCGGAGCTTCCCAATAT ** * 102698337 -TGGCTTGCTTGAACTTCCCAATAT 1 ATGGCTT-CCGGAGCTTCCCAATAT 102698361 ATGGCTATCCGGAGCTTCCC 1 ATGGCT-TCCGGAGCTTCCC 102698381 GTTAATGGCT Statistics Matches: 35, Mismatches: 6, Indels: 6 0.74 0.13 0.13 Matches are distributed among these distances: 23 1 0.03 24 19 0.54 25 14 0.40 26 1 0.03 ACGTcount: A:0.19, C:0.30, G:0.20, T:0.30 Consensus pattern (24 bp): ATGGCTTCCGGAGCTTCCCAATAT Found at i:102698398 original size:24 final size:24 Alignment explanation

Indices: 102698372--102698501 Score: 66 Period size: 24 Copynumber: 5.3 Consensus size: 24 102698362 TGGCTATCCG 102698372 GAGCTTCCCGTTAATGGCTC-TAT 1 GAGCTTCCCGTTAATGGCTCGTAT * ** * * 102698395 GGAGCTACTTGTTATTGGCTCGCAT 1 -GAGCTTCCCGTTAATGGCTCGTAT * * 102698420 GAGCTTCCTGATT-ATGGCTCTTAT 1 GAGCTTCCCG-TTAATGGCTCGTAT * ** * ** 102698444 GAGCTTTCCGTTATACAGCCCGGGT 1 GAGCTTCCCGTTA-ATGGCTCGTAT * ** 102698469 AAGCTTCCCGTTACATGGCTCACAT 1 GAGCTTCCCGTTA-ATGGCTCGTAT 102698494 GAGCTTCC 1 GAGCTTCC 102698502 TATATATGGC Statistics Matches: 74, Mismatches: 28, Indels: 7 0.68 0.26 0.06 Matches are distributed among these distances: 23 2 0.03 24 40 0.54 25 32 0.43 ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33 Consensus pattern (24 bp): GAGCTTCCCGTTAATGGCTCGTAT Found at i:102698860 original size:17 final size:17 Alignment explanation

Indices: 102698816--102698861 Score: 53 Period size: 15 Copynumber: 2.9 Consensus size: 17 102698806 GAAATACATG * 102698816 GAAATG-ATGGTAT-AT 1 GAAATGAATGATATAAT * 102698831 GAAAT-ATTGATATAAT 1 GAAATGAATGATATAAT 102698847 GAAATGAATGATATA 1 GAAATGAATGATATA 102698862 TGTTTATGAA Statistics Matches: 25, Mismatches: 3, Indels: 4 0.78 0.09 0.12 Matches are distributed among these distances: 15 10 0.40 16 7 0.28 17 8 0.32 ACGTcount: A:0.48, C:0.00, G:0.20, T:0.33 Consensus pattern (17 bp): GAAATGAATGATATAAT Found at i:102702815 original size:39 final size:40 Alignment explanation

Indices: 102702637--102702819 Score: 181 Period size: 40 Copynumber: 4.6 Consensus size: 40 102702627 CCGCACCAAG * * * * * * * * 102702637 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT 1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT * * * 102702677 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAA-T 1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCAC-AATT * 102702717 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT 1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT * * * * 102702757 GCCTTCGGGTCTTAACCCGGATATAATTTC-AGCATAATT 1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT * * 102702796 GTCTTCGGGGCTTAGCCCGGATAT 1 GCCTTCGGGTCTTAGCCCGGATAT 102702820 CATTCAATTT Statistics Matches: 122, Mismatches: 19, Indels: 5 0.84 0.13 0.03 Matches are distributed among these distances: 39 31 0.25 40 89 0.73 41 2 0.02 ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28 Consensus pattern (40 bp): GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT Found at i:102710877 original size:39 final size:40 Alignment explanation

Indices: 102710699--102710881 Score: 181 Period size: 40 Copynumber: 4.6 Consensus size: 40 102710689 CCGCACCAAG * * * * * * * * 102710699 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT 1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT * * * 102710739 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAA-T 1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCAC-AATT * 102710779 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT 1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT * * * * 102710819 GCCTTCGGGTCTTAACCCGGATATAATTTC-AGCATAATT 1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT * * 102710858 GTCTTCGGGGCTTAGCCCGGATAT 1 GCCTTCGGGTCTTAGCCCGGATAT 102710882 CATTCAATTT Statistics Matches: 122, Mismatches: 19, Indels: 5 0.84 0.13 0.03 Matches are distributed among these distances: 39 31 0.25 40 89 0.73 41 2 0.02 ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28 Consensus pattern (40 bp): GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT Found at i:102719353 original size:28 final size:28 Alignment explanation

Indices: 102719288--102719388 Score: 114 Period size: 28 Copynumber: 3.5 Consensus size: 28 102719278 ATAGTGAATC * 102719288 CGCACACTTAGTGCTATATGTATTC-AACT 1 CGCACACTTAGTGCTATA--TAATCAAACT 102719317 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTATATAATCAAACT * * * * 102719345 CGCACACTTAGTGCTGTACAATTTTAAACC 1 CGCACACTTAGTGCTATATAA--TCAAACT 102719375 CGCACACTTAGTGC 1 CGCACACTTAGTGC 102719389 CAATCTTGTC Statistics Matches: 64, Mismatches: 5, Indels: 5 0.86 0.07 0.07 Matches are distributed among these distances: 27 4 0.06 28 23 0.36 29 18 0.28 30 19 0.30 ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30 Consensus pattern (28 bp): CGCACACTTAGTGCTATATAATCAAACT Found at i:102724098 original size:29 final size:29 Alignment explanation

Indices: 102724066--102724200 Score: 157 Period size: 29 Copynumber: 4.7 Consensus size: 29 102724056 ATACCCTTCG ** * * 102724066 AGCTCGCACACCCAGTGCCGTATTTTTCC 1 AGCTCGCACACTTAGTGCCATATATTTCC * * * 102724095 AGCTTGCACACATAGTGTCATAT-TTTCC 1 AGCTCGCACACTTAGTGCCATATATTTCC * 102724123 AGCAT-GCACACTTAGTGCCTTATATTTCC 1 AGC-TCGCACACTTAGTGCCATATATTTCC * 102724152 AGCACGCACACTTAGTGCCATATATTTCC 1 AGCTCGCACACTTAGTGCCATATATTTCC * 102724181 AGCACGCACACTTAGTGCCA 1 AGCTCGCACACTTAGTGCCA 102724201 ATCTCGTCAC Statistics Matches: 93, Mismatches: 10, Indels: 6 0.85 0.09 0.06 Matches are distributed among these distances: 28 23 0.25 29 70 0.75 ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29 Consensus pattern (29 bp): AGCTCGCACACTTAGTGCCATATATTTCC Found at i:102724151 original size:57 final size:58 Alignment explanation

Indices: 102724041--102724199 Score: 176 Period size: 57 Copynumber: 2.8 Consensus size: 58 102724031 AATTTAAGCC * *** * * ** * * 102724041 CGCACACACAGTGCCATACCCTTCGAGCTCGCACACCCAGTGCCGTATTTTTCCAGCT 1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA * * * * 102724099 TGCACACATAGTGTCATAT-TTTCCAGCATGCACACTTAGTGCCTTATATTTCCAGCA 1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA * 102724156 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCC 1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCC 102724200 AATCTCGTCA Statistics Matches: 83, Mismatches: 17, Indels: 2 0.81 0.17 0.02 Matches are distributed among these distances: 57 45 0.54 58 38 0.46 ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27 Consensus pattern (58 bp): CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA Found at i:102726130 original size:203 final size:203 Alignment explanation

Indices: 102725773--102726182 Score: 624 Period size: 203 Copynumber: 2.0 Consensus size: 203 102725763 TTATCCTGAT * * * * 102725773 AGCTAAGCATGACAACCATTTATCGATTAAAATAAAGGTGTTCAACCCTTAAAAACCCATAATCC 1 AGCTAAGCATGACAACCATTTATAGATTAAAATAAAGGTGTTCAAACCGTAAAAACCCAGAATCC * * * * * 102725838 GTAATTATACAGAAGCTTTTAAGAGTTCCTACTCTACTTCTCTCTTTAATTCGCAAGTACAGAGA 66 ATAATTATACAGAAGCTTTTAAGAGTTCCTACTCTACTTCTCTCTTCAATCCACAAGTACAGAAA * * * * 102725903 GGTAAGGAAGTTTACCAATTCCTCAACTTCTCTACTACCAGACTTCAATTCTCATGATGGTTGCG 131 GGTAAGGAAATTCACCAATTCCTCAACTTCTCTACTACCAGACTTCAATTCTCATGACGATTGCG 102725968 ACATGCAA 196 ACATGCAA * * 102725976 AGCTAAGCATGACAACCATTTATTAG-TTAAACTAAAGGTGTTCAAACCGTAAAAATCCAGAATC 1 AGCTAAGCATGACAACCATTTA-TAGATTAAAATAAAGGTGTTCAAACCGTAAAAACCCAGAATC * * * 102726040 CATAATTATATAGAAGCTTTTAAGTGTTCTTACTCTACTTCTCTCTTCAATCCACAAGTACAGAA 65 CATAATTATACAGAAGCTTTTAAGAGTTCCTACTCTACTTCTCTCTTCAATCCACAAGTACAGAA * 102726105 AGGTAAGGAAATTCACCAGTTCCTCAACTTCTCTACTACCAGACTTCAATTCTCATGACGATTGC 130 AGGTAAGGAAATTCACCAATTCCTCAACTTCTCTACTACCAGACTTCAATTCTCATGACGATTGC * 102726170 GACATGCAG 195 GACATGCAA 102726179 AGCT 1 AGCT 102726183 TCTTTCAGCT Statistics Matches: 186, Mismatches: 20, Indels: 2 0.89 0.10 0.01 Matches are distributed among these distances: 203 184 0.99 204 2 0.01 ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30 Consensus pattern (203 bp): AGCTAAGCATGACAACCATTTATAGATTAAAATAAAGGTGTTCAAACCGTAAAAACCCAGAATCC ATAATTATACAGAAGCTTTTAAGAGTTCCTACTCTACTTCTCTCTTCAATCCACAAGTACAGAAA GGTAAGGAAATTCACCAATTCCTCAACTTCTCTACTACCAGACTTCAATTCTCATGACGATTGCG ACATGCAA Found at i:102728217 original size:48 final size:48 Alignment explanation

Indices: 102728146--102728269 Score: 158 Period size: 48 Copynumber: 2.6 Consensus size: 48 102728136 AAGCTAATGC * * * * 102728146 CATGTCCTAGATAGGTCTTACACTAGCTTGTATATCTCGAGGCTGATG 1 CATGTCCTAGACATGTCTTACACTAGCTTATATATCTCGAGGCCGATG * * 102728194 CATGTCCTAGACATGTCTTACACTGGTTTATATATCTCGAGGCCGATG 1 CATGTCCTAGACATGTCTTACACTAGCTTATATATCTCGAGGCCGATG * * * * 102728242 TATGTCCCAGACATGTGTTACATTAGCT 1 CATGTCCTAGACATGTCTTACACTAGCT 102728270 CTCATAATGT Statistics Matches: 64, Mismatches: 12, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 48 64 1.00 ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34 Consensus pattern (48 bp): CATGTCCTAGACATGTCTTACACTAGCTTATATATCTCGAGGCCGATG Found at i:102732281 original size:2 final size:2 Alignment explanation

Indices: 102732274--102732309 Score: 65 Period size: 2 Copynumber: 18.5 Consensus size: 2 102732264 CAAACAGGCA 102732274 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 102732310 CCATATCACA Statistics Matches: 33, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 1 1 0.03 2 32 0.97 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:102733612 original size:28 final size:26 Alignment explanation

Indices: 102733566--102733625 Score: 75 Period size: 28 Copynumber: 2.2 Consensus size: 26 102733556 GGCTAAGTTC 102733566 AATTTATTTTTTAATTATTAATATAT 1 AATTTATTTTTTAATTATTAATATAT * * * 102733592 TATTTATTTATTTTATATATTATTATAT 1 AATTTATTT-TTTAAT-TATTAATATAT 102733620 AATTTA 1 AATTTA 102733626 AATAACATAC Statistics Matches: 28, Mismatches: 4, Indels: 2 0.82 0.12 0.06 Matches are distributed among these distances: 26 8 0.29 27 5 0.18 28 15 0.54 ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63 Consensus pattern (26 bp): AATTTATTTTTTAATTATTAATATAT Found at i:102733624 original size:20 final size:20 Alignment explanation

Indices: 102733569--102733624 Score: 60 Period size: 20 Copynumber: 2.7 Consensus size: 20 102733559 TAAGTTCAAT * 102733569 TTATTTTTTAATTATTAATATA 1 TTATTTATTAATT-TT-ATATA * 102733591 TTATTTATTTATTTTATATA 1 TTATTTATTAATTTTATATA 102733611 TTA-TTATATAATTT 1 TTATTTAT-TAATTT 102733625 AAATAACATA Statistics Matches: 30, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 19 4 0.13 20 13 0.43 21 2 0.07 22 11 0.37 ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66 Consensus pattern (20 bp): TTATTTATTAATTTTATATA Found at i:102736302 original size:4 final size:4 Alignment explanation

Indices: 102736287--102736316 Score: 51 Period size: 4 Copynumber: 7.2 Consensus size: 4 102736277 GCCTTAAAAC 102736287 TAAA TGAAA TAAA TAAA TAAA TAAA TAAA T 1 TAAA T-AAA TAAA TAAA TAAA TAAA TAAA T 102736317 GATTGTTTAT Statistics Matches: 25, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 4 21 0.84 5 4 0.16 ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27 Consensus pattern (4 bp): TAAA Found at i:102736310 original size:12 final size:13 Alignment explanation

Indices: 102736287--102736318 Score: 57 Period size: 12 Copynumber: 2.5 Consensus size: 13 102736277 GCCTTAAAAC 102736287 TAAATGAAATAAA 1 TAAATGAAATAAA 102736300 TAAAT-AAATAAA 1 TAAATGAAATAAA 102736312 TAAATGA 1 TAAATGA 102736319 TTGTTTATTT Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 12 12 0.67 13 6 0.33 ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25 Consensus pattern (13 bp): TAAATGAAATAAA Found at i:102737866 original size:13 final size:13 Alignment explanation

Indices: 102737848--102737889 Score: 61 Period size: 13 Copynumber: 3.3 Consensus size: 13 102737838 TTTCACAAAT 102737848 TATTATTATTTTA 1 TATTATTATTTTA 102737861 TATTATTA-TTTA 1 TATTATTATTTTA 102737873 TA-TATTATTGTTA 1 TATTATTATT-TTA 102737886 TATT 1 TATT 102737890 TTTACTCGTA Statistics Matches: 26, Mismatches: 0, Indels: 5 0.84 0.00 0.16 Matches are distributed among these distances: 11 5 0.19 12 7 0.27 13 13 0.50 14 1 0.04 ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67 Consensus pattern (13 bp): TATTATTATTTTA Found at i:102737867 original size:16 final size:16 Alignment explanation

Indices: 102737782--102737870 Score: 63 Period size: 16 Copynumber: 5.1 Consensus size: 16 102737772 CTTATTTTTA 102737782 TATTTTATATTA-TAT 1 TATTTTATATTATTAT * * 102737797 AATTATTCTATTATATAT 1 TATT-TTATATTAT-TAT 102737815 TATTTGTATTATTATTTAT 1 TATTT-TA-TATTA-TTAT * 102737834 TATTTTTCACAAATTATTAT 1 TA-TTTT---ATATTATTAT 102737854 TATTTTATATTATTAT 1 TATTTTATATTATTAT 102737870 T 1 T 102737871 TATATATTAT Statistics Matches: 58, Mismatches: 6, Indels: 19 0.70 0.07 0.23 Matches are distributed among these distances: 15 3 0.05 16 17 0.29 17 1 0.02 18 7 0.12 19 15 0.26 20 10 0.17 21 4 0.07 22 1 0.02 ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63 Consensus pattern (16 bp): TATTTTATATTATTAT Found at i:102737880 original size:30 final size:30 Alignment explanation

Indices: 102737773--102737886 Score: 83 Period size: 33 Copynumber: 3.7 Consensus size: 30 102737763 TCTTTTTACC * * 102737773 TTATTTTTATATT-TTA-TATTATATAATTA 1 TTATTTATATATTATTATTATTTTAT-ATTA * 102737802 TTCTATTATATATTATT-TGTATTATTAT-TTA 1 TTAT-TTATATATTATTAT-TATT-TTATATTA * * 102737833 TTATTTTTCACAAATTATTATTATTTTATATTA 1 TTA--TTT-ATATATTATTATTATTTTATATTA * 102737866 TTATTTATATATTATTGTTAT 1 TTATTTATATATTATTATTAT 102737887 ATTTTTACTC Statistics Matches: 66, Mismatches: 9, Indels: 19 0.70 0.10 0.20 Matches are distributed among these distances: 29 3 0.05 30 20 0.30 31 10 0.15 32 10 0.15 33 22 0.33 34 1 0.02 ACGTcount: A:0.32, C:0.03, G:0.02, T:0.64 Consensus pattern (30 bp): TTATTTATATATTATTATTATTTTATATTA Found at i:102741846 original size:29 final size:29 Alignment explanation

Indices: 102741792--102741848 Score: 71 Period size: 29 Copynumber: 2.0 Consensus size: 29 102741782 GTGACGAGAT * ** 102741792 TGGCACTGAGTGTGCGAGCTTGAAATGTA 1 TGGCACTAAGTGTGCGAGAGTGAAATGTA 102741821 TGGCACTAAGTGTGCGAGAAGT-AAATGT 1 TGGCACTAAGTGTGCGAG-AGTGAAATGT 102741849 GTACGGTGAC Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 29 23 0.96 30 1 0.04 ACGTcount: A:0.28, C:0.12, G:0.33, T:0.26 Consensus pattern (29 bp): TGGCACTAAGTGTGCGAGAGTGAAATGTA Found at i:102741867 original size:72 final size:72 Alignment explanation

Indices: 102741750--102741910 Score: 313 Period size: 72 Copynumber: 2.2 Consensus size: 72 102741740 GTTTGCTTTC * 102741750 GGCACTAAGTGTGCGAGAAGTAAATGTGTACGGTGACGAGATTGGCACTGAGTGTGCGAGCTTGA 1 GGCACTAAGTGTGCGAGAAGTAAATGTGTACGGTGACGAGATTGGCACTGAGTGTGAGAGCTTGA 102741815 AATGTAT 66 AATGTAT 102741822 GGCACTAAGTGTGCGAGAAGTAAATGTGTACGGTGACGAGATTGGCACTGAGTGTGAGAGCTTGA 1 GGCACTAAGTGTGCGAGAAGTAAATGTGTACGGTGACGAGATTGGCACTGAGTGTGAGAGCTTGA 102741887 AATGTAT 66 AATGTAT 102741894 GGCACTAAGTGTGCGAG 1 GGCACTAAGTGTGCGAG 102741911 TTTGGACTAT Statistics Matches: 88, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 72 88 1.00 ACGTcount: A:0.28, C:0.12, G:0.35, T:0.24 Consensus pattern (72 bp): GGCACTAAGTGTGCGAGAAGTAAATGTGTACGGTGACGAGATTGGCACTGAGTGTGAGAGCTTGA AATGTAT Found at i:102741923 original size:29 final size:29 Alignment explanation

Indices: 102741864--102741966 Score: 109 Period size: 29 Copynumber: 3.6 Consensus size: 29 102741854 GTGACGAGAT * * * 102741864 TGGCACTGAGTGTGAGAGCTTGAAATGTA 1 TGGCACTAAGTGTGCGAGCTTGAAATATA * * * 102741893 TGGCACTAAGTGTGCGAGTTTGGACTATA 1 TGGCACTAAGTGTGCGAGCTTGAAATATA * * * 102741922 TGGCACTATGTGTGCGGGCTT-AAATCACA 1 TGGCACTAAGTGTGCGAGCTTGAAAT-ATA 102741951 TGGCACTAAGTGTGCG 1 TGGCACTAAGTGTGCG 102741967 TGATCGAGTA Statistics Matches: 60, Mismatches: 13, Indels: 2 0.80 0.17 0.03 Matches are distributed among these distances: 28 2 0.03 29 58 0.97 ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28 Consensus pattern (29 bp): TGGCACTAAGTGTGCGAGCTTGAAATATA Found at i:102753881 original size:206 final size:206 Alignment explanation

Indices: 102753520--102754411 Score: 1396 Period size: 206 Copynumber: 4.3 Consensus size: 206 102753510 GCAGATCTGG * 102753520 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGTAAATCGAAGACATAGCTG 1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG 102753585 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA 66 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA * * 102753650 GAACAAATCAAAGTCTGGCATCTCCATATTCGACGGAGGGTAGACACATAGCAGATCTCACCTTC 131 GAACAAATCGAAGTCTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTCACCTTC 102753715 AGATGATTTCA 196 AGATGATTTCA * * * * 102753726 CTGAAGTAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATTGAAGACATAGCTG 1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG * ** * 102753791 ATTTGGCTTTCACGTGTTTACGACGAAGTAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA 66 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA * * * 102753856 GAACAAATCGAAGTCTGGCATCTCCATATTTGACGGAGAGCAGACACCTAGCAGATCTCACCTTC 131 GAACAAATCGAAGTCTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTCACCTTC 102753921 AGATGATTTCA 196 AGATGATTTCA * * 102753932 CTGAAGCAGATCTAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAACTG 1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG * 102753997 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCACA 66 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA 102754062 GAACAAATCGAAGTCTGGCATCT-C-TACTTCGACGGAGGGCAGACACATAGCAGATC-CAACCT 131 GAACAAATCGAAGTCTGGCATCTCCATA-TTCGACGGAGGGCAGACACATAGCAGATCTC-ACCT 102754124 TCAGATGATTAT-A 194 TCAGATGATT-TCA **** * * 102754137 CTGTTTTAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAATGAGCAAATCGAAGACATAGCTG 1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG * * 102754202 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAGTCTAAGATGATTTGGCATCTTTGTATTGTCAGA 66 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA * * * * * * * 102754267 AAACAAATTGAGGTTTGGCGTCTCCATATTCGACGGAGGGTAGACACATAGCAGATCTAACCTTC 131 GAACAAATCGAAGTCTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTCACCTTC ** 102754332 AGATGATTAGA 196 AGATGATTTCA * * * 102754343 CTGAAGCAGATCTAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGTAAATCGAAGACATAGCTG 1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG 102754408 ATTT 66 ATTT 102754412 AGTTTTCGTG Statistics Matches: 625, Mismatches: 54, Indels: 14 0.90 0.08 0.02 Matches are distributed among these distances: 204 3 0.00 205 179 0.29 206 441 0.71 207 2 0.00 ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29 Consensus pattern (206 bp): CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA GAACAAATCGAAGTCTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTCACCTTC AGATGATTTCA Found at i:102754296 original size:411 final size:412 Alignment explanation

Indices: 102753520--102754411 Score: 1432 Period size: 411 Copynumber: 2.2 Consensus size: 412 102753510 GCAGATCTGG * 102753520 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGTAAATCGAAGACATAGCTG 1 CTGAAGCAGATCTAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGTAAATCGAAGACATAGCTG * 102753585 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA 66 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCACA * 102753650 GAACAAATCAAAGTCTGGCATCTCCATATTCGACGGAGGGTAGACACATAGCAGATCTCACCTTC 131 GAACAAATCAAAGTCTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTCACCTTC * 102753715 AGATGATTTCACTGAAGTAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATTGA 196 AGATGATTTCACTGAAGTAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGA * * 102753780 AGACATAGCTGATTTGGCTTTCACGTGTTTACGACGAAGTAAATCTAAGATGATTTGGCATCTCT 261 AGACATAGCTGATTTGGCTTTCACGTGCTTACGACGAAGCAAATCTAAGATGATTTGGCATCTCT * * * 102753845 GTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCATATTTGACGGAGAGCAGACACCTAGCAG 326 GTATTGTCAGAAAACAAATCGAAGTCTGGCATCTCCATATTCGACGGAGAGCAGACACATAGCAG * * 102753910 ATCTCACCTTCAGATGATTTCA 391 ATCTAACCTTCAGATGATTACA * * 102753932 CTGAAGCAGATCTAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAACTG 1 CTGAAGCAGATCTAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGTAAATCGAAGACATAGCTG 102753997 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCACA 66 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCACA * 102754062 GAACAAATCGAAGTCTGGCATCT-C-TACTTCGACGGAGGGCAGACACATAGCAGATC-CAACCT 131 GAACAAATCAAAGTCTGGCATCTCCATA-TTCGACGGAGGGCAGACACATAGCAGATCTC-ACCT *** * * * * 102754124 TCAGATGATTAT-ACTGTTTTAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAATGAGCAAAT 194 TCAGATGATT-TCACTGAAGTAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAAT ** * 102754188 CGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAGTCTAAGATGATTTGGCATC 258 CGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGACGAAGCAAATCTAAGATGATTTGGCATC * * * * * * * 102754253 TTTGTATTGTCAGAAAACAAATTGAGGTTTGGCGTCTCCATATTCGACGGAGGGTAGACACATAG 323 TCTGTATTGTCAGAAAACAAATCGAAGTCTGGCATCTCCATATTCGACGGAGAGCAGACACATAG * 102754318 CAGATCTAACCTTCAGATGATTAGA 388 CAGATCTAACCTTCAGATGATTACA * 102754343 CTGAAGCAGATCTAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGTAAATCGAAGACATAGCTG 1 CTGAAGCAGATCTAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGTAAATCGAAGACATAGCTG 102754408 ATTT 66 ATTT 102754412 AGTTTTCGTG Statistics Matches: 442, Mismatches: 35, Indels: 7 0.91 0.07 0.01 Matches are distributed among these distances: 410 3 0.01 411 290 0.66 412 149 0.34 ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29 Consensus pattern (412 bp): CTGAAGCAGATCTAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGTAAATCGAAGACATAGCTG ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCACA GAACAAATCAAAGTCTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTCACCTTC AGATGATTTCACTGAAGTAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGA AGACATAGCTGATTTGGCTTTCACGTGCTTACGACGAAGCAAATCTAAGATGATTTGGCATCTCT GTATTGTCAGAAAACAAATCGAAGTCTGGCATCTCCATATTCGACGGAGAGCAGACACATAGCAG ATCTAACCTTCAGATGATTACA Found at i:102754700 original size:12 final size:13 Alignment explanation

Indices: 102754678--102754706 Score: 51 Period size: 12 Copynumber: 2.3 Consensus size: 13 102754668 CCTTAAAACC 102754678 AAATAAAATAAAT 1 AAATAAAATAAAT 102754691 AAAT-AAATAAAT 1 AAATAAAATAAAT 102754703 AAAT 1 AAAT 102754707 GATTGTTTAT Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 12 12 0.75 13 4 0.25 ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24 Consensus pattern (13 bp): AAATAAAATAAAT Found at i:102756262 original size:16 final size:16 Alignment explanation

Indices: 102756177--102756265 Score: 63 Period size: 16 Copynumber: 5.1 Consensus size: 16 102756167 CTTATTTTTA 102756177 TATTTTATATTA-TAT 1 TATTTTATATTATTAT * * 102756192 AATTATTCTATTATATAT 1 TATT-TTATATTAT-TAT 102756210 TATTTGTATTATTATTTAT 1 TATTT-TA-TATTA-TTAT * 102756229 TATTTTTCACAAATTATTAT 1 TA-TTTT---ATATTATTAT 102756249 TATTTTATATTATTAT 1 TATTTTATATTATTAT 102756265 T 1 T 102756266 GTTATATTAT Statistics Matches: 58, Mismatches: 6, Indels: 19 0.70 0.07 0.23 Matches are distributed among these distances: 15 3 0.05 16 17 0.29 17 1 0.02 18 7 0.12 19 15 0.26 20 10 0.17 21 4 0.07 22 1 0.02 ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63 Consensus pattern (16 bp): TATTTTATATTATTAT Found at i:102756273 original size:11 final size:11 Alignment explanation

Indices: 102756259--102756284 Score: 52 Period size: 11 Copynumber: 2.4 Consensus size: 11 102756249 TATTTTATAT 102756259 TATTATTGTTA 1 TATTATTGTTA 102756270 TATTATTGTTA 1 TATTATTGTTA 102756281 TATT 1 TATT 102756285 TTTACTCGTA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 15 1.00 ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65 Consensus pattern (11 bp): TATTATTGTTA Found at i:102756702 original size:17 final size:16 Alignment explanation

Indices: 102756679--102756737 Score: 59 Period size: 17 Copynumber: 3.6 Consensus size: 16 102756669 CCAATATATT 102756679 TTATATTTTTATATAA 1 TTATATTTTTATATAA * 102756695 TTATTATTCTTATA-AA 1 TTA-TATTTTTATATAA 102756711 -TATACTTTTTATTATATA 1 TTATA-TTTTTA-TATA-A 102756729 TTATATTTT 1 TTATATTTT 102756738 AAATCTATTA Statistics Matches: 35, Mismatches: 2, Indels: 10 0.74 0.04 0.21 Matches are distributed among these distances: 14 2 0.06 15 7 0.20 16 7 0.20 17 10 0.29 18 5 0.14 19 4 0.11 ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63 Consensus pattern (16 bp): TTATATTTTTATATAA Found at i:102764058 original size:44 final size:45 Alignment explanation

Indices: 102763955--102764442 Score: 278 Period size: 44 Copynumber: 11.0 Consensus size: 45 102763945 GACTGTCATG * * * * 102763955 CTGATAT-TTCAATCTGCTCTCT-ATCGAACACAAAGACGCCAAAT 1 CTGATATCTTCGATCTGCTCTCTGA-CAAATACAGAGACGCCAAAT * * 102763999 CTGCTATCTTCGATCTGCTCTCTGAC-AATACAGAGAAGCCAAAT 1 CTGATATCTTCGATCTGCTCTCTGACAAATACAGAGACGCCAAAT * * * * 102764043 CTGATGTCTTTGATCTGCTC-CTTGAC-AATACAGGGATGCCAAAT 1 CTGATATCTTCGATCTGCTCTC-TGACAAATACAGAGACGCCAAAT * * * * * * * * ** 102764087 CAGCT-TCTTGGATTTGCTC-CTCGTCGAATACAAAGATGTTAAAT 1 CTGATATCTTCGATCTGCTCTCT-GACAAATACAGAGACGCCAAAT * * * * * 102764131 CT-ACTATC-TCTGATTTGCTCTCTAAC-CATACAGAGATGTCAAAT 1 CTGA-TATCTTC-GATCTGCTCTCTGACAAATACAGAGACGCCAAAT * * * 102764175 CTGCTATCCTCGATCTGCTCCCTGACAAATACAGAGACGCCAAAT 1 CTGATATCTTCGATCTGCTCTCTGACAAATACAGAGACGCCAAAT * * * * * * 102764220 CT-ACTATCTTTGATCTACTGTATTGTCAAATACAGAGATGCCAAAT 1 CTGA-TATCTTCGATCTGCTCT-CTGACAAATACAGAGACGCCAAAT * * * * * 102764266 C----ATCTTAGATTTGCT-TCAG-CGTAAATAC-GTGAAAGCCAAAT 1 CTGATATCTTCGATCTGCTCTCTGAC--AAATACAGAG-ACGCCAAAT * * * * * 102764307 CTGCTATGTCTCCGATCTACTCCCTGAC-AATACAGGGACGCCAAAT 1 CTG--ATATCTTCGATCTGCTCTCTGACAAATACAGAGACGCCAAAT * * * * 102764353 CTGCTATCTTCGATCTGCTCTCTGACAAATATAGATACACCAAAT 1 CTGATATCTTCGATCTGCTCTCTGACAAATACAGAGACGCCAAAT * * 102764398 CTGCTATCTTTGATCTGCTCTCTGAC-AATACAGAGACGCCAAAT 1 CTGATATCTTCGATCTGCTCTCTGACAAATACAGAGACGCCAAAT 102764442 C 1 C 102764443 ATCTTAGATT Statistics Matches: 345, Mismatches: 72, Indels: 54 0.73 0.15 0.11 Matches are distributed among these distances: 39 1 0.00 40 3 0.01 41 16 0.05 42 12 0.03 43 16 0.05 44 145 0.42 45 97 0.28 46 41 0.12 47 11 0.03 48 2 0.01 49 1 0.00 ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30 Consensus pattern (45 bp): CTGATATCTTCGATCTGCTCTCTGACAAATACAGAGACGCCAAAT Found at i:102764279 original size:176 final size:172 Alignment explanation

Indices: 102763988--102764505 Score: 513 Period size: 176 Copynumber: 2.9 Consensus size: 172 102763978 TCGAACACAA * * 102763988 AGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGAC-AATACAGAGAAGCCAAATCTGA-TGTC 1 AGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAAATACAGAGACGCCAAATCT-ACTATC * * * ** * 102764051 TTTGATCTGCTCCTTGACAATACAGGGATGCCAAATCAGCTTCTTGGATTTGCTCCTCGTCGAAT 65 TTTGATCTGCT-TTTGACAATACAGAGATGCCAAATCA---TCTTAGATTTGCTCAGCGT-AAAT ** * * * * * 102764116 AC-AAAGATGTTAAATCTACTA-TCTCTGATTTGCTCTCTAACCATACAG 125 ACGAAA-A-GCCAAATCTACTAGTCTCCGATCTACTCCCTAACAATACAG * * * * 102764164 AGATGTCAAATCTGCTATCCTCGATCTGCTCCCTGACAAATACAGAGACGCCAAATCTACTATCT 1 AGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAAATACAGAGACGCCAAATCTACTATCT * * 102764229 TTGATCTACTGTATTGTCAAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAATAC 66 TTGATCTGCT-T-TTGAC-AATACAGAGATGCCAAATCATCTTAGATTTGC-TCAGCGTAAATAC * * * 102764294 GTGAAAGCCAAATCTGCTATGTCTCCGATCTACTCCCTGACAATACAG 127 G-AAAAGCCAAATCTACTA-GTCTCCGATCTACTCCCTAACAATACAG * * * * * 102764342 GGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAAATATAGATACACCAAATCTGCTATCT 1 AGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAAATACAGAGACGCCAAATCTACTATCT * * * * 102764407 TTGATCTGCTCTCTGACAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAGCATAAACACGT 66 TTGATCTGCT-TTTGACAATACAGAGATGCCAAATCATCTTAGATTTGC-TCAGCGTAAATACG- * * * * 102764472 GAAAGCCAAATCTGCTATGTCTTCGATCTGCTCC 128 AAAAGCCAAATCTACTA-GTCTCCGATCTACTCC 102764506 TTGTAAAAAT Statistics Matches: 290, Mismatches: 43, Indels: 18 0.83 0.12 0.05 Matches are distributed among these distances: 176 137 0.47 177 41 0.14 178 93 0.32 179 19 0.07 ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30 Consensus pattern (172 bp): AGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAAATACAGAGACGCCAAATCTACTATCT TTGATCTGCTTTTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTCAGCGTAAATACGAAA AGCCAAATCTACTAGTCTCCGATCTACTCCCTAACAATACAG Found at i:102764339 original size:87 final size:86 Alignment explanation

Indices: 102764248--102764505 Score: 285 Period size: 89 Copynumber: 2.9 Consensus size: 86 102764238 TGTATTGTCA * 102764248 AATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAATACGTGAAAGCCAAATCTGCTA 1 AATACAGAGACGCCAAATCATCTTAGATTTGCTTCAGC-TAAATACGTGAAAGCCAAATCTGCTA * * 102764313 TGTCTCCGATCTACTCCCTGAC 65 TGTCTTCGATCTGCTCCCTGAC * * * * 102764335 AATACAGGGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGAC-AAATA--TAGATACA-CCAA 1 AATACAGAGACGCCAAA--T-C-ATCTTAGATTTGCT-TCAG-CTAAATACGT-GA-A-AGCCAA * * 102764396 ATCTGCTA--TCTTTGATCTGCTCTCTGAC 57 ATCTGCTATGTCTTCGATCTGCTCCCTGAC * 102764424 AATACAGAGACGCCAAATCATCTTAGATTTGCTTCAGCATAAACACGTGAAAGCCAAATCTGCTA 1 AATACAGAGACGCCAAATCATCTTAGATTTGCTTCAGC-TAAATACGTGAAAGCCAAATCTGCTA 102764489 TGTCTTCGATCTGCTCC 65 TGTCTTCGATCTGCTCC 102764506 TTGTAAAAAT Statistics Matches: 139, Mismatches: 16, Indels: 32 0.74 0.09 0.17 Matches are distributed among these distances: 83 1 0.01 84 4 0.03 85 29 0.21 86 3 0.02 87 30 0.22 89 34 0.24 90 3 0.02 91 30 0.22 92 4 0.03 93 1 0.01 ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28 Consensus pattern (86 bp): AATACAGAGACGCCAAATCATCTTAGATTTGCTTCAGCTAAATACGTGAAAGCCAAATCTGCTAT GTCTTCGATCTGCTCCCTGAC Found at i:102764528 original size:176 final size:178 Alignment explanation

Indices: 102764158--102764529 Score: 518 Period size: 176 Copynumber: 2.1 Consensus size: 178 102764148 CTCTCTAACC * * * 102764158 ATACAGAGATGTCAAATCTGCTATCCTCGATCTGCTCCCTGACAAATACAGAGACGCCAAATCTA 1 ATACAGGGATGCCAAATCTGCTATCCTCGATCTGCTCCCTGACAAATACAGAGACACCAAATCTA * * * * * 102764223 CTATCTTTGATCTACTGTATTGTCAAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGT 66 CTATCTTTGATCTACTCTACTGACAAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAGCAT * * 102764288 AAATACGTGAAAGCCAAATCTGCTATGTCTCCGATCTACTCCCTGACA 131 AAACACGTGAAAGCCAAATCTGCTATGTCTCCGATCTACTCCCTGAAA * * * * * * 102764336 ATACAGGGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAAATATAGATACACCAAATCTG 1 ATACAGGGATGCCAAATCTGCTATCCTCGATCTGCTCCCTGACAAATACAGAGACACCAAATCTA * 102764401 CTATCTTTGATCTGCTCT-CTGAC-AATACAGAGACGCCAAATCATCTTAGATTTGCTTCAGCAT 66 CTATCTTTGATCTACTCTACTGACAAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAGCAT * * * 102764464 AAACACGTGAAAGCCAAATCTGCTATGTCTTCGATCTGCTCCTTGTAAAA 131 AAACACGTGAAAGCCAAATCTGCTATGTCTCCGATCTACTCCCTG--AAA 102764514 ATA-A-GGATGCCAAATC 1 ATACAGGGATGCCAAATC 102764530 ATCTTGGATC Statistics Matches: 171, Mismatches: 21, Indels: 6 0.86 0.11 0.03 Matches are distributed among these distances: 176 90 0.53 177 4 0.02 178 77 0.45 ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28 Consensus pattern (178 bp): ATACAGGGATGCCAAATCTGCTATCCTCGATCTGCTCCCTGACAAATACAGAGACACCAAATCTA CTATCTTTGATCTACTCTACTGACAAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAGCAT AAACACGTGAAAGCCAAATCTGCTATGTCTCCGATCTACTCCCTGAAA Found at i:102764530 original size:87 final size:87 Alignment explanation

Indices: 102764247--102764534 Score: 279 Period size: 87 Copynumber: 3.3 Consensus size: 87 102764237 CTGTATTGTC * * 102764247 AAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAATACGTGAAAGCCAAATCTGCT 1 AAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAGCATAAATACGTGAAAGCCAAATCTGCT * * * 102764312 ATGTCTCCGATCTACTCCCTGA 66 ATGTCTTCGATCTGCTCCTTGA * * * * * * 102764334 CAATACAGGGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACA-AATATA-GAT-ACA-CCA 1 AAATACAGAGACGCCAAA--T-C-ATCTTAGATTTGCT-TCAG-CATAA-ATACG-TGAAAGCCA * 102764395 AATCTGCTA--TCTTTGATCTGCT-CTCTGA 58 AATCTGCTATGTCTTCGATCTGCTCCT-TGA * * 102764423 CAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAGCATAAACACGTGAAAGCCAAATCTGCT 1 AAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAGCATAAATACGTGAAAGCCAAATCTGCT 102764488 ATGTCTTCGATCTGCTCCTTGTAA 66 ATGTCTTCGATCTGCTCCTTG--A * 102764512 AAATA-AG-GATGCCAAATCATCTT 1 AAATACAGAGACGCCAAATCATCTT 102764535 GGATCTACTT Statistics Matches: 162, Mismatches: 21, Indels: 36 0.74 0.10 0.16 Matches are distributed among these distances: 83 5 0.03 84 8 0.05 85 24 0.15 86 1 0.01 87 45 0.28 88 5 0.03 89 36 0.22 90 1 0.01 91 24 0.15 92 8 0.05 93 5 0.03 ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28 Consensus pattern (87 bp): AAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAGCATAAATACGTGAAAGCCAAATCTGCT ATGTCTTCGATCTGCTCCTTGA Found at i:102771600 original size:13 final size:13 Alignment explanation

Indices: 102771584--102771609 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 102771574 TCACTATCCT 102771584 TTCTTCCTATGGC 1 TTCTTCCTATGGC 102771597 TTCTTCCTATGGC 1 TTCTTCCTATGGC 102771610 CGAATATGCA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.08, C:0.31, G:0.15, T:0.46 Consensus pattern (13 bp): TTCTTCCTATGGC Found at i:102776920 original size:40 final size:40 Alignment explanation

Indices: 102776861--102777028 Score: 198 Period size: 40 Copynumber: 4.2 Consensus size: 40 102776851 TGGAATACAA * * 102776861 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACGACTCGCACGAATGCCTTCGGGTCTTAGC * * 102776901 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGC 1 CCGGATATAACGACTCGCACGAATGCCTTCGGGTCTTAGC * * * 102776941 CCAGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACGACTCGCACGAATGCCTTCGGGTCTTAGC * * 102776981 CCGGATA-AA-GTCACTAGCAC-AATTGCCTTCGGGTCTTAAC 1 CCGGATATAACG--ACTCGCACGAA-TGCCTTCGGGTCTTAGC * 102777021 CCGAATAT 1 CCGGATAT 102777029 CATTCAATTG Statistics Matches: 110, Mismatches: 14, Indels: 7 0.84 0.11 0.05 Matches are distributed among these distances: 39 4 0.04 40 106 0.96 ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23 Consensus pattern (40 bp): CCGGATATAACGACTCGCACGAATGCCTTCGGGTCTTAGC Found at i:102784747 original size:29 final size:29 Alignment explanation

Indices: 102784712--102784904 Score: 305 Period size: 29 Copynumber: 6.7 Consensus size: 29 102784702 ATAAACGATC *** * 102784712 TCGCACACTTAGTGCCATGCGATTTAAGC 1 TCGCACACTTAGTGCCATATAATTTAAGT * 102784741 TCGCACACATAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT * 102784770 TTGCACACTTAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT * 102784799 TCGCACACCTAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT 102784828 TCGCACACTTAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT * 102784857 TTGCACACTTAGTGCCATATAATTTAAGT 1 TCGCACACTTAGTGCCATATAATTTAAGT * 102784886 TTGCACACTTAGTGCCATA 1 TCGCACACTTAGTGCCATA 102784905 CCTTCCAAGC Statistics Matches: 153, Mismatches: 11, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 29 153 1.00 ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33 Consensus pattern (29 bp): TCGCACACTTAGTGCCATATAATTTAAGT Found at i:102784815 original size:87 final size:87 Alignment explanation

Indices: 102784712--102784931 Score: 325 Period size: 87 Copynumber: 2.5 Consensus size: 87 102784702 ATAAACGATC * * 102784712 TCGCACACTTAGTGCCATGCGATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTTGCACA 1 TCGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTTGCACA 102784777 CTTAGTGCCATATAATTTAAGT 66 CTTAGTGCCATATAATTTAAGT * * * * 102784799 TCGCACACCTAGTGCCATATAATTTAAGTTCGCACACTTAGTGCCATATAATTTAAGTTTGCACA 1 TCGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTTGCACA 102784864 CTTAGTGCCATATAATTTAAGT 66 CTTAGTGCCATATAATTTAAGT * * * * * 102784886 TTGCACACTTAGTGCCATAC-CTTCCAAGCCCGCACACTTAGTGCCA 1 TCGCACACTTAGTGCCATACAATT-TAAGCTCGCACACATAGTGCCA 102784932 ATCTTGTCAC Statistics Matches: 119, Mismatches: 13, Indels: 2 0.89 0.10 0.01 Matches are distributed among these distances: 86 2 0.02 87 117 0.98 ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31 Consensus pattern (87 bp): TCGCACACTTAGTGCCATACAATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTTGCACA CTTAGTGCCATATAATTTAAGT Found at i:102784921 original size:58 final size:58 Alignment explanation

Indices: 102784714--102784931 Score: 303 Period size: 58 Copynumber: 3.8 Consensus size: 58 102784704 AAACGATCTC *** * 102784714 GCACACTTAGTGCCATGCGATTTAAGCTCGCACACATAGTGCCATATAATTTAAGTTT 1 GCACACTTAGTGCCATATAATTTAAGCTCGCACACTTAGTGCCATATAATTTAAGTTT * * * 102784772 GCACACTTAGTGCCATATAATTTAAGTTCGCACACCTAGTGCCATATAATTTAAGTTC 1 GCACACTTAGTGCCATATAATTTAAGCTCGCACACTTAGTGCCATATAATTTAAGTTT * * 102784830 GCACACTTAGTGCCATATAATTTAAGTTTGCACACTTAGTGCCATATAATTTAAGTTT 1 GCACACTTAGTGCCATATAATTTAAGCTCGCACACTTAGTGCCATATAATTTAAGTTT ** * * 102784888 GCACACTTAGTGCCATA-CCTTCCAAGCCCGCACACTTAGTGCCA 1 GCACACTTAGTGCCATATAATT-TAAGCTCGCACACTTAGTGCCA 102784932 ATCTTGTCAC Statistics Matches: 144, Mismatches: 15, Indels: 2 0.89 0.09 0.01 Matches are distributed among these distances: 57 2 0.01 58 142 0.99 ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31 Consensus pattern (58 bp): GCACACTTAGTGCCATATAATTTAAGCTCGCACACTTAGTGCCATATAATTTAAGTTT Found at i:102786011 original size:31 final size:31 Alignment explanation

Indices: 102785973--102786034 Score: 124 Period size: 31 Copynumber: 2.0 Consensus size: 31 102785963 TTCAAGAGTG 102785973 GCATAAAACATACCTTCTTGTATCAAAACAC 1 GCATAAAACATACCTTCTTGTATCAAAACAC 102786004 GCATAAAACATACCTTCTTGTATCAAAACAC 1 GCATAAAACATACCTTCTTGTATCAAAACAC 102786035 CTTAGTCTAG Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 31 31 1.00 ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26 Consensus pattern (31 bp): GCATAAAACATACCTTCTTGTATCAAAACAC Found at i:102788200 original size:40 final size:40 Alignment explanation

Indices: 102788155--102788322 Score: 198 Period size: 40 Copynumber: 4.2 Consensus size: 40 102788145 CGGAATACAA 102788155 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC * * * * 102788195 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGC 1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC * * ** 102788235 CCAGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC * * 102788275 CCGGATA-AAGTCACTA-GCAC-AATTGCCTTCGGGTCTTAAC 1 CCGGATATAA-CCAC-ACGCACGAA-TGCCTTCGGGTCTTAGC 102788315 CCGGATAT 1 CCGGATAT 102788323 CATTCAATTG Statistics Matches: 110, Mismatches: 14, Indels: 7 0.84 0.11 0.05 Matches are distributed among these distances: 39 4 0.04 40 106 0.96 ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23 Consensus pattern (40 bp): CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC Found at i:102788295 original size:80 final size:80 Alignment explanation

Indices: 102788171--102788322 Score: 227 Period size: 80 Copynumber: 1.9 Consensus size: 80 102788161 ATAACCACAC * * 102788171 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGCC 1 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATGCCTTCGGGTATTAACC 102788236 CAGATATAACAACTT 66 CAGATATAACAACTT * * 102788251 GCACGAATGCCTTCGGGTCTTAGCCCGGATA-AA-GTCACTAGCACAATTGCCTTCGGGTCTTAA 1 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAACG--ACTAGCACAAATGCCTTCGGGTATTAA * 102788314 CCCGGATAT 64 CCCAGATAT 102788323 CATTCAATTG Statistics Matches: 65, Mismatches: 5, Indels: 4 0.88 0.07 0.05 Matches are distributed among these distances: 78 1 0.02 79 2 0.03 80 62 0.95 ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24 Consensus pattern (80 bp): GCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATGCCTTCGGGTATTAACC CAGATATAACAACTT Found at i:102793506 original size:40 final size:40 Alignment explanation

Indices: 102793413--102793589 Score: 182 Period size: 40 Copynumber: 4.5 Consensus size: 40 102793403 AAGCCAAGTA * * * * 102793413 CCTTCGGGATTTA-ACCAGATATAGCT-ACTCGCTC-AATG 1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG * * 102793451 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG * * * * 102793491 CCTTCAGGACTTAGCCCGGATATAGTAGCTCGTAGAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG * * * 102793531 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG 1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG * 102793571 CCTTCGGAACTTAGCCCGG 1 CCTTCGGGACTTAGCCCGG 102793590 TTATCATCTG Statistics Matches: 116, Mismatches: 19, Indels: 6 0.82 0.13 0.04 Matches are distributed among these distances: 38 12 0.10 39 17 0.15 40 87 0.75 ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23 Consensus pattern (40 bp): CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG Found at i:102798842 original size:47 final size:49 Alignment explanation

Indices: 102798791--102798996 Score: 145 Period size: 47 Copynumber: 4.2 Consensus size: 49 102798781 ACAAAAAAGA * * * 102798791 TGTGATATGTGCTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTG 1 TGTGATATGTGCTTCCGTATAAGACCATAGATGGGCTATGGCATC-G-ATG * ** 102798842 ATGTGATAATGTGCTTTCGTATAAGACCATTTATGGGAC-ATGGCATC-A-G 1 -TGTGAT-ATGTGCTTCCGTATAAGACCATAGATGGG-CTATGGCATCGATG * * * * * * 102798891 TATTATATGTGCTTCTGTGTAAGACCATATATGGGATATGGCATC-A-G 1 TGTGATATGTGCTTCCGTATAAGACCATAGATGGGCTATGGCATCGATG * * * * * * * * 102798938 TGTGATATGTG-ATACGTGTAAGACCATGGCTGAGCTATGGCTTCGGTG 1 TGTGATATGTGCTTCCGTATAAGACCATAGATGGGCTATGGCATCGATG 102798986 TGTGATATGTG 1 TGTGATATGTG 102798997 ACTATGTACA Statistics Matches: 124, Mismatches: 25, Indels: 14 0.76 0.15 0.09 Matches are distributed among these distances: 46 24 0.19 47 44 0.35 48 16 0.13 49 1 0.01 52 6 0.05 53 32 0.26 54 1 0.01 ACGTcount: A:0.24, C:0.15, G:0.29, T:0.33 Consensus pattern (49 bp): TGTGATATGTGCTTCCGTATAAGACCATAGATGGGCTATGGCATCGATG Found at i:102798885 original size:53 final size:51 Alignment explanation

Indices: 102798789--102798943 Score: 151 Period size: 47 Copynumber: 3.1 Consensus size: 51 102798779 TGACAAAAAA ** ** 102798789 GATGTGATATGTGCTCCCGTATAAGACCATAGCTGGG-CTATGGCATCGGTGT 1 GATGTGATATGTGCTTTCGTATAAGACCATATATGGGAC-ATGGCATC-GTGT * * 102798841 GATGTGATAATGTGCTTTCGTATAAGACCATTTATGGGACATGGCATC-AGT 1 GATGTGAT-ATGTGCTTTCGTATAAGACCATATATGGGACATGGCATCGTGT * * 102798892 -AT-T-ATATGTGC-TTCTGTGTAAGACCATATATGGGATATGGCATCAGTGT 1 GATGTGATATGTGCTTTC-GTATAAGACCATATATGGGACATGGCATC-GTGT 102798941 GAT 1 GAT 102798944 ATGTGATACG Statistics Matches: 87, Mismatches: 10, Indels: 14 0.78 0.09 0.13 Matches are distributed among these distances: 46 3 0.03 47 32 0.37 48 2 0.02 49 3 0.03 50 4 0.05 51 2 0.02 52 8 0.09 53 32 0.37 54 1 0.01 ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33 Consensus pattern (51 bp): GATGTGATATGTGCTTTCGTATAAGACCATATATGGGACATGGCATCGTGT Found at i:102801995 original size:127 final size:127 Alignment explanation

Indices: 102801858--102802141 Score: 442 Period size: 127 Copynumber: 2.2 Consensus size: 127 102801848 CCCATCATGG * * 102801858 TAGGGCACGATTCCTTGAATTTCCAAACATTGAACATTGCCTTGCTTTAGAATTTAGAAAACACG 1 TAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTTGCTTTAAAATTTAGAAAACACG 102801923 AGTGAAATTCAAAAGAAATATTCGATTATTTTGAACAAACGGGAAATCAAAACCCAGCACGA 66 AGTGAAATTCAAAAGAAATATTCGATTATTTTGAACAAACGGGAAATCAAAACCCAGCACGA * * * * * 102801985 TAGGGCACGATTCCCCGAATTTCCAAACATTGAACATTGTCTTGTTTTAAAATTTGGGAAACACG 1 TAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTTGCTTTAAAATTTAGAAAACACG * * * * 102802050 AGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGGGAAATCGAAACCCAGCACGG 66 AGTGAAATTCAAAAGAAATATTCGATTATTTTGAACAAACGGGAAATCAAAACCCAGCACGA * * * 102802112 TAGGGCACAATTCCTCGAGTTCCCAAACAT 1 TAGGGCACGATTCCTCGAATTTCCAAACAT 102802142 CAATCATTAC Statistics Matches: 142, Mismatches: 15, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 127 142 1.00 ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26 Consensus pattern (127 bp): TAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTTGCTTTAAAATTTAGAAAACACG AGTGAAATTCAAAAGAAATATTCGATTATTTTGAACAAACGGGAAATCAAAACCCAGCACGA Found at i:102805444 original size:25 final size:24 Alignment explanation

Indices: 102805416--102805519 Score: 73 Period size: 25 Copynumber: 3.9 Consensus size: 24 102805406 AAAGTTTACA * 102805416 ACAATAATATAAAATAATGATATGT 1 ACAAAAATATAAAATAAT-ATATGT * 102805441 ACAAAAATATATATATATATACATATGT 1 ACAAAAATATA-A-A-ATA-ATATATGT * * * 102805469 ACATAAAATATACACTAATATATAT 1 ACA-AAAATATAAAATAATATATGT 102805494 ACATAATATATATAAAATACATATAT 1 ACA-AA-A-ATATAAAATA-ATATAT 102805520 ATATATATAT Statistics Matches: 63, Mismatches: 8, Indels: 13 0.75 0.10 0.15 Matches are distributed among these distances: 25 22 0.35 26 4 0.06 27 10 0.16 28 18 0.29 29 9 0.14 ACGTcount: A:0.56, C:0.08, G:0.03, T:0.34 Consensus pattern (24 bp): ACAAAAATATAAAATAATATATGT Found at i:102805454 original size:2 final size:2 Alignment explanation

Indices: 102805447--102805530 Score: 59 Period size: 2 Copynumber: 43.5 Consensus size: 2 102805437 ATGTACAAAA * * * * * 102805447 AT AT AT AT AT AT AT AC AT AT GT AC AT A- AA AT AT AC ACT A- AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT * * * 102805488 AT AT AT AC AT A- AT AT AT AT A- AA AT AC AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 102805528 AT A 1 AT A 102805531 CGTATTAGAA Statistics Matches: 63, Mismatches: 14, Indels: 10 0.72 0.16 0.11 Matches are distributed among these distances: 1 4 0.06 2 58 0.92 3 1 0.02 ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38 Consensus pattern (2 bp): AT Found at i:102805506 original size:15 final size:16 Alignment explanation

Indices: 102805447--102805524 Score: 61 Period size: 15 Copynumber: 4.7 Consensus size: 16 102805437 ATGTACAAAA * 102805447 ATATATATATATATAC 1 ATATATATATAAATAC * * 102805463 ATATGTACATAAAATATAC 1 ATA--TATATATAA-ATAC * 102805482 ACTAATATATATACATA- 1 A-T-ATATATATAAATAC 102805499 ATATATATA-AAATAC 1 ATATATATATAAATAC 102805514 ATATATATATA 1 ATATATATATA 102805525 TATATACGTA Statistics Matches: 48, Mismatches: 7, Indels: 14 0.70 0.10 0.20 Matches are distributed among these distances: 14 4 0.08 15 16 0.33 16 5 0.10 17 1 0.02 18 9 0.19 19 11 0.23 20 1 0.02 21 1 0.02 ACGTcount: A:0.54, C:0.08, G:0.01, T:0.37 Consensus pattern (16 bp): ATATATATATAAATAC Found at i:102805866 original size:11 final size:11 Alignment explanation

Indices: 102805833--102805873 Score: 50 Period size: 11 Copynumber: 3.9 Consensus size: 11 102805823 AAATCATTTT 102805833 GAAGAGAGAAA 1 GAAGAGAGAAA * 102805844 GAA-A-AAAAA 1 GAAGAGAGAAA * 102805853 GAAGGGAGAAA 1 GAAGAGAGAAA 102805864 GAAGAGAGAA 1 GAAGAGAGAA 102805874 GGGATGGGGG Statistics Matches: 24, Mismatches: 4, Indels: 4 0.75 0.12 0.12 Matches are distributed among these distances: 9 7 0.29 10 1 0.04 11 16 0.67 ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00 Consensus pattern (11 bp): GAAGAGAGAAA Found at i:102807138 original size:30 final size:30 Alignment explanation

Indices: 102807102--102807160 Score: 93 Period size: 30 Copynumber: 2.0 Consensus size: 30 102807092 TTTGAAAAAT 102807102 AGAAATT-AAAAGACTCAACTCAACTCTCGC 1 AGAAATTAAAAAG-CTCAACTCAACTCTCGC * 102807132 AGAAATTAAAAAGCTCAACTCACCTCTCG 1 AGAAATTAAAAAGCTCAACTCAACTCTCG 102807161 TAATATGAGT Statistics Matches: 27, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 30 22 0.81 31 5 0.19 ACGTcount: A:0.42, C:0.27, G:0.10, T:0.20 Consensus pattern (30 bp): AGAAATTAAAAAGCTCAACTCAACTCTCGC Found at i:102807198 original size:87 final size:84 Alignment explanation

Indices: 102807062--102807219 Score: 244 Period size: 87 Copynumber: 1.8 Consensus size: 84 102807052 GACTAGAGGT * 102807062 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAAAAGACTCAACTCAACT 1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACT 102807127 CTCGCAGAAATTAAAAAGC 66 CTCGCAGAAATTAAAAAGC * * * 102807146 TCAACTCACCTCTCGTAATATGAGTTGAATTTTTTTGAAAAACAGAAATTAAAAGGCTTAACTCA 1 TCAACTCACCTCTCGCAATATGAGTTG-A--TTTTTGAAAAACAGAAATTAAAAGACTCAACTCA * 102807211 CCTCTCGCA 63 ACTCTCGCA 102807220 ACATGAGTTG Statistics Matches: 66, Mismatches: 5, Indels: 3 0.89 0.07 0.04 Matches are distributed among these distances: 84 26 0.39 85 1 0.02 87 39 0.59 ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28 Consensus pattern (84 bp): TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACT CTCGCAGAAATTAAAAAGC Found at i:102807226 original size:57 final size:55 Alignment explanation

Indices: 102807131--102807252 Score: 165 Period size: 57 Copynumber: 2.2 Consensus size: 55 102807121 TCAACTCTCG * * 102807131 CAGAAATTAAAAAGCTCAACTCACCTCTCGTAATATGAGTTGAATTTTTTTGAAA-AA 1 CAGAAATTAAAAAGCTCAACTCACCTCTCGCAACATGAGTTG-A--TTTTTGAAACAA * * 102807188 CAGAAATTAAAAGGCTTAACTCACCTCTCGCAACATGAGTTGATTTTTGAAACAA 1 CAGAAATTAAAAAGCTCAACTCACCTCTCGCAACATGAGTTGATTTTTGAAACAA * 102807243 CAAAAATTAA 1 CAGAAATTAA 102807253 GAATACCTCA Statistics Matches: 59, Mismatches: 5, Indels: 4 0.87 0.07 0.06 Matches are distributed among these distances: 54 9 0.15 55 11 0.19 56 1 0.02 57 38 0.64 ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29 Consensus pattern (55 bp): CAGAAATTAAAAAGCTCAACTCACCTCTCGCAACATGAGTTGATTTTTGAAACAA Found at i:102807585 original size:73 final size:72 Alignment explanation

Indices: 102807492--102807681 Score: 256 Period size: 72 Copynumber: 2.6 Consensus size: 72 102807482 ATTAAAAGGT * * * * * * * * 102807492 TCAACCCACCTCTCGCAATATAAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGT 1 TCAACTCACCTCTAGCAATATGAGTTGATT-TTGAAAAACAAAAATTGAAAATACCTCAGCGTGC 102807557 CCTGAGGC 65 CCTGAGGC ** 102807565 TCAACTCACCTCTAGCAATATGAGTTGAAATT-AAAACACAAAAATTGAAAATACCTCAGCGTGC 1 TCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAA-ACAAAAATTGAAAATACCTCAGCGTGC 102807629 CCTGAGGC 65 CCTGAGGC * 102807637 TCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACCAAAAT 1 TCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAAT 102807682 AAAAAGGCTT Statistics Matches: 102, Mismatches: 13, Indels: 5 0.85 0.11 0.04 Matches are distributed among these distances: 71 3 0.03 72 70 0.69 73 29 0.28 ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26 Consensus pattern (72 bp): TCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTGAAAATACCTCAGCGTGCC CTGAGGC Found at i:102808023 original size:76 final size:77 Alignment explanation

Indices: 102807864--102808009 Score: 231 Period size: 76 Copynumber: 1.9 Consensus size: 77 102807854 TTGAAAAACG * * 102807864 GAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATACGAGTTGATTT 1 GAAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATTT 102807929 TTTTTTGACAACA 65 TTTTTTGACAACA * * * 102807942 GAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT 1 GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATTTT 102808006 TTTT 66 TTTT 102808010 GAAAGGCAGA Statistics Matches: 63, Mismatches: 5, Indels: 2 0.90 0.07 0.03 Matches are distributed among these distances: 76 41 0.65 78 22 0.35 ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32 Consensus pattern (77 bp): GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATTTT TTTTTGACAACA Found at i:102808086 original size:169 final size:167 Alignment explanation

Indices: 102807801--102808517 Score: 1125 Period size: 169 Copynumber: 4.2 Consensus size: 167 102807791 AAAAATTAAA * ** * 102807801 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTTTTTTTGAAAGGCAGAAATTGAAAAACGGA 1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAAAACGAA * * 102807866 AATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATACGAGTTGATTTTT 66 AATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGA--TTT 102807931 TTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTG 129 TTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTG 102807970 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTGAAAGGCAGAAATTTGAAAAACGA 1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAA-TTGAAAAACGA * * 102808034 AAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT 65 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT * * * * * 102808098 TTTGAAAGACAGAAATTGAAAATAGCTCAGTGCGTGAGCC-A 130 TTTGACA-ACAGAAATTGAAATTACCTCA--GCGTG-TCCTG * 102808139 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAGGCAGAAATTGAAAAACG 1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTTTGAAAGGCAGAAATTGAAAAACG * 102808204 AAAATTGAAAATACCTCGGCATGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTT 64 AAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGA--T * 102808269 TTTTTTTACAACAGAAATTGAAATTACCTCAGCGTGTCCTG 127 TTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTG 102808310 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTTGAAAAACGA 1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAA-TTGAAAAACGA * * * 102808375 AAATTGAAAATACCTCGACGTGTGACTTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTT 65 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT * 102808440 TTTGACAACAGAAATTGAAATTACCTCAGCATGTCCTG 130 TTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTG 102808478 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTT 1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTT 102808518 AAAATACCTC Statistics Matches: 505, Mismatches: 30, Indels: 27 0.90 0.05 0.05 Matches are distributed among these distances: 166 9 0.02 167 19 0.04 168 100 0.20 169 153 0.30 170 72 0.14 171 105 0.21 172 20 0.04 173 19 0.04 174 8 0.02 ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30 Consensus pattern (167 bp): AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAAAACGAA AATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTT TTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTG Found at i:102808111 original size:91 final size:89 Alignment explanation

Indices: 102807943--102808272 Score: 321 Period size: 91 Copynumber: 3.7 Consensus size: 89 102807933 TTGACAACAG * 102807943 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT 1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTT * 102808008 TTGAAAGGCAGAAATTTGAAAAACGA 65 TTGAAAGACAGAAA-TTGAAAAACGA * * 102808034 AAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT 1 AAATTGAAAATACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT 102808098 TTTGAAAGACAGAAATT-------GA 64 TTTGAAAGACAGAAATTGAAAAACGA ** * * * * 102808117 AAA-T--AGCT-CAGT--GCGTGAGCC-AAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTT 1 AAATTGAAAATAC-CTCAGCGTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---- * 102808175 TTTTTTTGAAAGGCAGAAATTGAAAAACGA 60 TTTTTTTGAAAGACAGAAATTGAAAAACGA * * * 102808205 AAATTGAAAATACCTCGGCATGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT 1 AAATTGAAAATACCTCAGC--GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT 102808270 TTT 64 TTT 102808273 TTTACAACAG Statistics Matches: 195, Mismatches: 19, Indels: 50 0.74 0.07 0.19 Matches are distributed among these distances: 76 31 0.16 77 1 0.01 78 5 0.03 79 1 0.01 80 3 0.02 81 19 0.10 82 1 0.01 83 5 0.03 88 5 0.03 89 1 0.01 90 2 0.01 91 48 0.25 92 1 0.01 93 37 0.19 94 2 0.01 95 33 0.17 ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30 Consensus pattern (89 bp): AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT TGAAAGACAGAAATTGAAAAACGA Found at i:102808242 original size:340 final size:339 Alignment explanation

Indices: 102807800--102808517 Score: 1196 Period size: 340 Copynumber: 2.1 Consensus size: 339 102807790 CAAAAATTAA * * 102807800 AAGGCTTAACTCACCTCTCGCAATATGAG-TCA-ATTTTTTTTTGAAAGGCAGAAATTGAAAAAC 1 AAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAGGCAGAAATTGAAAAAC * * * 102807863 GGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATACGAGTTGATT 66 GAAAATTGAAAATACCTCGGCATGTGACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATT 102807928 TTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT 131 TTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT * 102807993 ATGAGTTGA-TTTTTTTTGAAAGGCAGAAATTTGAAAAACGAAAATTGAAAATACCTCGGCGTGT 196 ATGAGTTGATTTTTTTTTGAAAGGCAGAAATTTGAAAAACGAAAATTGAAAATACCTCGACGTGT * 102808057 GA-TCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAGACAGAAATTGAAAA 261 GACT-TGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAAA-ACAGAAATTGAAAA * * 102808120 TAGCTCAGTGCGTGAGCC- 324 TACCTCA--GCATG-GCCT 102808138 AAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAGGCAGAAATTGAAAAAC 1 AAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAGGCAGAAATTGAAAAAC * 102808203 GAAAATTGAAAATACCTCGGCATGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATT 66 GAAAATTGAAAATACCTCGGCATGTGACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATT * 102808268 TTTTTTTTACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT 131 TTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT 102808333 ATGAGTTGATTTTTTTTTGAAAGGCAGAAATTTGAAAAACGAAAATTGAAAATACCTCGACGTGT 196 ATGAGTTGATTTTTTTTTGAAAGGCAGAAATTTGAAAAACGAAAATTGAAAATACCTCGACGTGT * * * 102808398 GACTTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGACAACAGAAATTGAAATTA 261 GACTTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAAAACAGAAATTGAAAATA * 102808463 CCTCAGCATGTCCT 326 CCTCAGCATGGCCT * * 102808477 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTT 1 AAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTT 102808518 AAAATACCTC Statistics Matches: 357, Mismatches: 17, Indels: 11 0.93 0.04 0.03 Matches are distributed among these distances: 338 31 0.09 339 45 0.13 340 164 0.46 341 107 0.30 342 10 0.03 ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30 Consensus pattern (339 bp): AAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAGGCAGAAATTGAAAAAC GAAAATTGAAAATACCTCGGCATGTGACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATT TTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT ATGAGTTGATTTTTTTTTGAAAGGCAGAAATTTGAAAAACGAAAATTGAAAATACCTCGACGTGT GACTTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAAAACAGAAATTGAAAATA CCTCAGCATGGCCT Found at i:102808333 original size:76 final size:77 Alignment explanation

Indices: 102808205--102808350 Score: 240 Period size: 76 Copynumber: 1.9 Consensus size: 77 102808195 TGAAAAACGA * 102808205 AAATTGAAAATACCTCGGCATGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT 1 AAATTGAAAATACCTCAGCA-GTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT 102808270 TTTTTTACAACAG 65 TTTTTTACAACAG * * * 102808283 AAATTGAAATTACCTCAGC-GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT 1 AAATTGAAAATACCTCAGCAGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTT 102808347 TTTT 66 TTTT 102808351 GAAAGGCAGA Statistics Matches: 64, Mismatches: 4, Indels: 2 0.91 0.06 0.03 Matches are distributed among these distances: 76 47 0.73 78 17 0.27 ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34 Consensus pattern (77 bp): AAATTGAAAATACCTCAGCAGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTT TTTTTACAACAG Found at i:102808556 original size:61 final size:61 Alignment explanation

Indices: 102808461--102808575 Score: 203 Period size: 61 Copynumber: 1.9 Consensus size: 61 102808451 AAATTGAAAT * * 102808461 TACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAA 1 TACCTCAGCACGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAA * 102808522 TACCTCAGCGCGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT 1 TACCTCAGCACGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT 102808576 GAAACATACG Statistics Matches: 51, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 61 51 1.00 ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33 Consensus pattern (61 bp): TACCTCAGCACGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAA Found at i:102808627 original size:137 final size:135 Alignment explanation

Indices: 102808404--102808651 Score: 363 Period size: 137 Copynumber: 1.8 Consensus size: 135 102808394 GTGTGACTTG * *** * * 102808404 AGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAG 1 AGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTGAAACAACAAAAATTGAAATTAACTCAG * * 102808469 CATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAATACCTCAGCGCG 66 CATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTAAAATACCTCAGCGCG 102808534 TCCTA 131 TCCTA * 102808539 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATACGAAAAATTGACAA-TAACT 1 AGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTGAAACA-AC-AAAAATTGA-AATTAACT * * 102808603 CAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGATTTGAATTTT 63 CAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTT 102808652 GAAATAAAAC Statistics Matches: 99, Mismatches: 11, Indels: 4 0.87 0.10 0.04 Matches are distributed among these distances: 135 38 0.38 136 2 0.02 137 57 0.58 138 2 0.02 ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30 Consensus pattern (135 bp): AGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTGAAACAACAAAAATTGAAATTAACTCAG CATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTAAAATACCTCAGCGCG TCCTA Found at i:102818770 original size:2 final size:2 Alignment explanation

Indices: 102818763--102818846 Score: 59 Period size: 2 Copynumber: 43.5 Consensus size: 2 102818753 ATGTACAAAA * * * * * 102818763 AT AT AT AT AT AT AT AT AT AT AC AT AT GT AC AT A- AA AT AT AC 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT * * * 102818804 ACT A- AT AT AT AT AC AT A- AT AT AT AT A- AA AT AC AT AT AT AT 1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 102818844 AT A 1 AT A 102818847 CGTATTAGAA Statistics Matches: 63, Mismatches: 14, Indels: 10 0.72 0.16 0.11 Matches are distributed among these distances: 1 4 0.06 2 58 0.92 3 1 0.02 ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38 Consensus pattern (2 bp): AT Found at i:102818790 original size:34 final size:33 Alignment explanation

Indices: 102818751--102818846 Score: 104 Period size: 34 Copynumber: 2.8 Consensus size: 33 102818741 TAAAATAATG * 102818751 ATATGTACAAAAATATATATATATATATATATA 1 ATATGTACAAAAATATATATATATATATACATA * 102818784 CATATGTACATAAAATATACACTAATATATATACATA 1 -ATATGTACA-AAAATATATA-T-ATATATATACATA * * * 102818821 ATATATA-TAAAATACATATATATATA 1 ATATGTACAAAAATATATATATATATA 102818847 CGTATTAGAA Statistics Matches: 53, Mismatches: 6, Indels: 8 0.79 0.09 0.12 Matches are distributed among these distances: 32 7 0.13 33 1 0.02 34 17 0.32 35 9 0.17 36 7 0.13 37 12 0.23 ACGTcount: A:0.54, C:0.07, G:0.02, T:0.36 Consensus pattern (33 bp): ATATGTACAAAAATATATATATATATATACATA Found at i:102820315 original size:10 final size:10 Alignment explanation

Indices: 102820300--102820325 Score: 52 Period size: 10 Copynumber: 2.6 Consensus size: 10 102820290 ATGATAAGAA 102820300 GAGAGAAAAT 1 GAGAGAAAAT 102820310 GAGAGAAAAT 1 GAGAGAAAAT 102820320 GAGAGA 1 GAGAGA 102820326 GATGTGTATT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 16 1.00 ACGTcount: A:0.58, C:0.00, G:0.35, T:0.08 Consensus pattern (10 bp): GAGAGAAAAT Found at i:102828901 original size:23 final size:24 Alignment explanation

Indices: 102828870--102828925 Score: 64 Period size: 24 Copynumber: 2.3 Consensus size: 24 102828860 AGAGAGAATA 102828870 TTATATTAA-A-TAATTATTTAATTT 1 TTATATTAATATTAA-T-TTTAATTT 102828894 TTAT-TTAATATTAATTTTAATTTT 1 TTATATTAATATTAATTTTAA-TTT 102828918 TTATATTA 1 TTATATTA 102828926 CTAAAAATGT Statistics Matches: 28, Mismatches: 0, Indels: 7 0.80 0.00 0.20 Matches are distributed among these distances: 23 9 0.32 24 13 0.46 25 6 0.21 ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62 Consensus pattern (24 bp): TTATATTAATATTAATTTTAATTT Found at i:102831612 original size:95 final size:93 Alignment explanation

Indices: 102831505--102831733 Score: 280 Period size: 95 Copynumber: 2.5 Consensus size: 93 102831495 TTTTGCTCCC *** 102831505 TTAAAAAGTTAATTTTAATCCTACATTGGCTAGAGAACACTCCCACGCTCGCACTTGCTTTTTAA 1 TTAAAAAGTTAATTTTAATCCTACATTGGCTAGAGAACACTCCCACGCTCGCACTTGCTCAATAA * * * 102831570 ATAAGCGTTAGCTTTTTTTTACTATTTTCA 66 ATAAGCATTA-C-TTTCTTCACTATTTTCA * * * * * * 102831600 TTAAAAAGTTAATTTTAATCTTACATTGGCTAGAAAACCCTCTCATGCTCGCATTTGCTCAATAA 1 TTAAAAAGTTAATTTTAATCCTACATTGGCTAGAGAACACTCCCACGCTCGCACTTGCTCAATAA * 102831665 ATAAGTATTACTTTCTTCACTATTTTCA 66 ATAAGCATTACTTTCTTCACTATTTTCA * * * * 102831693 TT-AAAAGTTTATTTTAATCCAATATTGACTAGAGAACACTC 1 TTAAAAAGTTAATTTTAATCCTACATTGGCTAGAGAACACTC 102831734 TTATATCTCA Statistics Matches: 114, Mismatches: 20, Indels: 3 0.83 0.15 0.02 Matches are distributed among these distances: 92 32 0.28 93 17 0.15 94 1 0.01 95 64 0.56 ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39 Consensus pattern (93 bp): TTAAAAAGTTAATTTTAATCCTACATTGGCTAGAGAACACTCCCACGCTCGCACTTGCTCAATAA ATAAGCATTACTTTCTTCACTATTTTCA Found at i:102831758 original size:93 final size:93 Alignment explanation

Indices: 102831508--102831792 Score: 234 Period size: 95 Copynumber: 3.0 Consensus size: 93 102831498 TGCTCCCTTA * * * * * * *** 102831508 AAAAGTTAATTTTAATCCTACATTGGCTAGAGAACACTCCCACGCTCGCACTT-GCTTTTTAAAT 1 AAAAGTTAATTTTAATCCAACATTGACTAGAAAACACTCTCATGCTCACA-TTAGCTCAATAAAT * * ** * * 102831572 AAGCGTTAGCTTTTTTTTACTATTTTCATT 65 AAGTGATA-AATTTCTTCACTATTTTCATT ** * * * * 102831602 AAAAAGTTAATTTTAATCTTACATTGGCTAGAAAACCCTCTCATGCTCGCATTTGCTCAATAAAT 1 -AAAAGTTAATTTTAATCCAACATTGACTAGAAAACACTCTCATGCTCACATTAGCTCAATAAAT * * 102831667 AAGT-ATTACTTTCTTCACTATTTTCATT 65 AAGTGATAAATTTCTTCACTATTTTCATT * * * * * * 102831695 AAAAGTTTATTTTAATCCAATATTGACTAGAGAACACTCTTATATCTCACATTGAGCT-TATAAA 1 AAAAGTTAATTTTAATCCAACATTGACTAGAAAACACTCTCAT-GCTCACATT-AGCTCAATAAA * 102831759 TAAGTGATAAATTTCTTCACTAATTTCATT 64 TAAGTGATAAATTTCTTCACTATTTTCATT 102831789 AAAA 1 AAAA 102831793 ATTTTATGTA Statistics Matches: 156, Mismatches: 30, Indels: 9 0.80 0.15 0.05 Matches are distributed among these distances: 92 35 0.22 93 34 0.22 94 31 0.20 95 56 0.36 ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39 Consensus pattern (93 bp): AAAAGTTAATTTTAATCCAACATTGACTAGAAAACACTCTCATGCTCACATTAGCTCAATAAATA AGTGATAAATTTCTTCACTATTTTCATT Found at i:102831947 original size:34 final size:34 Alignment explanation

Indices: 102831860--102831930 Score: 142 Period size: 34 Copynumber: 2.1 Consensus size: 34 102831850 CATCAACTCA 102831860 TTTGAGAAATTAATTATTTTACAGCGGAAAAATC 1 TTTGAGAAATTAATTATTTTACAGCGGAAAAATC 102831894 TTTGAGAAATTAATTATTTTACAGCGGAAAAATC 1 TTTGAGAAATTAATTATTTTACAGCGGAAAAATC 102831928 TTT 1 TTT 102831931 TCGGAATTTT Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 34 37 1.00 ACGTcount: A:0.39, C:0.08, G:0.14, T:0.38 Consensus pattern (34 bp): TTTGAGAAATTAATTATTTTACAGCGGAAAAATC Found at i:102838561 original size:40 final size:40 Alignment explanation

Indices: 102838503--102838770 Score: 376 Period size: 40 Copynumber: 6.7 Consensus size: 40 102838493 ATAACCACAA * * * * 102838503 GCACAATTGCCTTTGGGTCTTAACCCGGGTATAGCAACTC 1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC * 102838543 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC 1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC * * 102838583 GCACAAATGCCTTCAGGTCTTAACCCGGATATAGCAACTC 1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC * * 102838623 GCACAAATGCCTTTGGGTCTTAGCCCGGATATAACAACTC 1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC * * 102838663 GCACAAATGCCTTCAGGTCTTAACCCGGATATAGCAACTC 1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC * * * 102838703 ACACAAATGCCTTCGGGTCTTAGCCCGGATATAATC-ACTA 1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT-AGCAACTC * * 102838743 GCATAAATGCCTTCGGGGCTTAGCCCGG 1 GCACAAATGCCTTCGGGTCTTAGCCCGG 102838771 TATTATTCAA Statistics Matches: 203, Mismatches: 24, Indels: 2 0.89 0.10 0.01 Matches are distributed among these distances: 40 201 0.99 41 2 0.01 ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24 Consensus pattern (40 bp): GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC Found at i:102838588 original size:80 final size:80 Alignment explanation

Indices: 102838483--102838770 Score: 427 Period size: 80 Copynumber: 3.6 Consensus size: 80 102838473 TCTTCGGAAT * ** * ** * 102838483 TTAG-CCGGATATAACCACAAGCACAATTGCCTTTGGGTCTTAACCCGGGTATAGCAACTCGCAC 1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCAGGTCTTAACCCGGATATAGCAACTCGCAC 102838547 AAATGCCTTCGGGTC 66 AAATGCCTTCGGGTC 102838562 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCAGGTCTTAACCCGGATATAGCAACTCGCAC 1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCAGGTCTTAACCCGGATATAGCAACTCGCAC * 102838627 AAATGCCTTTGGGTC 66 AAATGCCTTCGGGTC * 102838642 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCAGGTCTTAACCCGGATATAGCAACTCACAC 1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCAGGTCTTAACCCGGATATAGCAACTCGCAC 102838707 AAATGCCTTCGGGTC 66 AAATGCCTTCGGGTC * * * * * 102838722 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGGCTTAGCCCGG 1 TTAGCCCGGATATAA-CAACTCGCACAAATGCCTTCAGGTCTTAACCCGG 102838771 TATTATTCAA Statistics Matches: 192, Mismatches: 15, Indels: 3 0.91 0.07 0.01 Matches are distributed among these distances: 79 4 0.02 80 187 0.97 81 1 0.01 ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24 Consensus pattern (80 bp): TTAGCCCGGATATAACAACTCGCACAAATGCCTTCAGGTCTTAACCCGGATATAGCAACTCGCAC AAATGCCTTCGGGTC Found at i:102846673 original size:32 final size:31 Alignment explanation

Indices: 102846605--102846673 Score: 95 Period size: 32 Copynumber: 2.2 Consensus size: 31 102846595 AACCACAAGC * 102846605 ACAA-TTGCCTTCGGGTCTTAACCCGGGTAT 1 ACAACTTGCCTTCGGGTCTTAACCCGGATAT * 102846635 AGCAACTTGCCTTCGGGTCTTAGCCCGGATAT 1 A-CAACTTGCCTTCGGGTCTTAACCCGGATAT 102846667 GACAACT 1 -ACAACT 102846674 CGCACAAATG Statistics Matches: 34, Mismatches: 2, Indels: 4 0.85 0.05 0.10 Matches are distributed among these distances: 30 1 0.03 31 3 0.09 32 29 0.85 33 1 0.03 ACGTcount: A:0.22, C:0.28, G:0.23, T:0.28 Consensus pattern (31 bp): ACAACTTGCCTTCGGGTCTTAACCCGGATAT Found at i:102846746 original size:40 final size:40 Alignment explanation

Indices: 102846642--102846858 Score: 320 Period size: 40 Copynumber: 5.5 Consensus size: 40 102846632 TATAGCAACT 102846642 TGCCTTCGGGTCTTAGCCCGGATAT-GACAACTCGCACAAA 1 TGCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAA * * 102846682 TGCCTTC-GGTCTTAACCCGAATATAGCAACTCGCACAAA 1 TGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAA * 102846721 TGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAA 1 TGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAA 102846761 TGCCTTCGGGTCTTA-CCCGGATATA-CAACTCGCACAAA 1 TGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAA * * * 102846799 TGCCTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAA 1 TGCCTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAA 102846839 TGCCTTCGGG-CTTAGCCCGG 1 TGCCTTCGGGTCTTAGCCCGG 102846859 GTATCATTCA Statistics Matches: 165, Mismatches: 7, Indels: 11 0.90 0.04 0.06 Matches are distributed among these distances: 38 28 0.17 39 64 0.39 40 72 0.44 41 1 0.01 ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24 Consensus pattern (40 bp): TGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAA Found at i:102846824 original size:78 final size:79 Alignment explanation

Indices: 102846642--102846858 Score: 343 Period size: 78 Copynumber: 2.8 Consensus size: 79 102846632 TATAGCAACT * * 102846642 TGCCTTCGGGTCTTAGCCCGGATATGACAACTCGCACAAATGCCTTC-GGTCTTAACCCGAATAT 1 TGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTT-ACCCGGATAT 102846706 AGCAACTCGCACAAA 65 AGCAACTCGCACAAA 102846721 TGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTACCCGGATATA 1 TGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTACCCGGATATA 102846786 -CAACTCGCACAAA 66 GCAACTCGCACAAA * * 102846799 TGCCTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGG-CTTAGCCCGG 1 TGCCTTCGGGTCTTAGCCCGGATATAA-CAACTCGCACAAATGCCTTCGGGTCTTA-CCCGG 102846859 GTATCATTCA Statistics Matches: 131, Mismatches: 4, Indels: 7 0.92 0.03 0.05 Matches are distributed among these distances: 77 4 0.03 78 64 0.49 79 57 0.44 80 6 0.05 ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24 Consensus pattern (79 bp): TGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTACCCGGATATA GCAACTCGCACAAA Found at i:102849466 original size:70 final size:70 Alignment explanation

Indices: 102849347--102849484 Score: 195 Period size: 70 Copynumber: 2.0 Consensus size: 70 102849337 ATATTACATT * * * 102849347 TTAATTTTAATCCCACATTGACTAAAGAATACTCTCATAACTCATTTCTTCACTATTTTCATTAA 1 TTAATTTTAATCCCACATTAACTAAAGAATACTCTCACAACTCACTTCTTCACTATTTTCATTAA 102849412 AAAAG 66 AAAAG * * * * * * 102849417 TTAATTTTAATCCTATATTAACTAGAGAATACTTTCACAACTCGCTTCTTTACTATTTTCATTAA 1 TTAATTTTAATCCCACATTAACTAAAGAATACTCTCACAACTCACTTCTTCACTATTTTCATTAA 102849482 AAA 66 AAA 102849485 TTAATATTAA Statistics Matches: 59, Mismatches: 9, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 70 59 1.00 ACGTcount: A:0.36, C:0.19, G:0.04, T:0.41 Consensus pattern (70 bp): TTAATTTTAATCCCACATTAACTAAAGAATACTCTCACAACTCACTTCTTCACTATTTTCATTAA AAAAG Found at i:102854680 original size:9 final size:9 Alignment explanation

Indices: 102854650--102854710 Score: 52 Period size: 9 Copynumber: 6.7 Consensus size: 9 102854640 CTTTTATATA * 102854650 TATACATTT 1 TATATATTT 102854659 TATATATAATT 1 TATATAT--TT * 102854670 TATTTATTT 1 TATATATTT * 102854679 TAAATATTT 1 TATATATTT * 102854688 TATATATAT 1 TATATATTT * 102854697 TATTTATTT 1 TATATATTT 102854706 T-TATA 1 TATATA 102854711 AATATTATTT Statistics Matches: 41, Mismatches: 9, Indels: 5 0.75 0.16 0.09 Matches are distributed among these distances: 8 3 0.07 9 30 0.73 11 8 0.20 ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62 Consensus pattern (9 bp): TATATATTT Found at i:102854697 original size:20 final size:22 Alignment explanation

Indices: 102854648--102854697 Score: 54 Period size: 20 Copynumber: 2.5 Consensus size: 22 102854638 TCCTTTTATA * 102854648 TATATACATTTTATATATAATT 1 TATATATATTTTATATATAATT * 102854670 TAT-T-TATTTTA-A-ATATTT 1 TATATATATTTTATATATAATT 102854688 TATATATATT 1 TATATATATT 102854698 ATTTATTTTT Statistics Matches: 24, Mismatches: 2, Indels: 6 0.75 0.06 0.19 Matches are distributed among these distances: 18 8 0.33 19 2 0.08 20 10 0.42 21 1 0.04 22 3 0.12 ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60 Consensus pattern (22 bp): TATATATATTTTATATATAATT Found at i:102854702 original size:31 final size:28 Alignment explanation

Indices: 102854655--102854716 Score: 88 Period size: 29 Copynumber: 2.1 Consensus size: 28 102854645 ATATATATAC * 102854655 ATTTTATATATAATTTATTTATTTTAAAT 1 ATTTTATATATAATTTATTT-TTATAAAT 102854684 ATTTTATATATATTATTTATTTTTATAAAT 1 ATTTTATATATA--ATTTATTTTTATAAAT 102854714 ATT 1 ATT 102854717 ATTTATACAT Statistics Matches: 30, Mismatches: 1, Indels: 3 0.88 0.03 0.09 Matches are distributed among these distances: 29 12 0.40 30 10 0.33 31 8 0.27 ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63 Consensus pattern (28 bp): ATTTTATATATAATTTATTTTTATAAAT Found at i:102854709 original size:19 final size:19 Alignment explanation

Indices: 102854685--102854722 Score: 67 Period size: 19 Copynumber: 2.0 Consensus size: 19 102854675 ATTTTAAATA * 102854685 TTTTATATATATTATTTAT 1 TTTTATAAATATTATTTAT 102854704 TTTTATAAATATTATTTAT 1 TTTTATAAATATTATTTAT 102854723 ACATGTAAAA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 19 18 1.00 ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66 Consensus pattern (19 bp): TTTTATAAATATTATTTAT Found at i:102854758 original size:19 final size:18 Alignment explanation

Indices: 102854736--102854840 Score: 60 Period size: 19 Copynumber: 5.7 Consensus size: 18 102854726 TGTAAAATTA 102854736 TTATATATAATATTTTTAT 1 TTATATAT-ATATTTTTAT * * 102854755 TTATGTAT-TATTTATCAT 1 TTATATATATATTT-TTAT 102854773 GTTAT-T-TATATTTTATAT 1 -TTATATATATATTTT-TAT * * 102854791 ATTTTATATATAGCTTTTA- 1 -TTATATATATA-TTTTTAT 102854810 TTATATATTATATATTTTA- 1 TTATATA-TATAT-TTTTAT 102854829 TTATATAT-TATT 1 TTATATATATATT 102854841 CCCTATATTA Statistics Matches: 69, Mismatches: 8, Indels: 21 0.70 0.08 0.21 Matches are distributed among these distances: 16 1 0.01 17 10 0.14 18 21 0.30 19 28 0.41 20 6 0.09 21 3 0.04 ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63 Consensus pattern (18 bp): TTATATATATATTTTTAT Found at i:102854790 original size:47 final size:51 Alignment explanation

Indices: 102854682--102854791 Score: 115 Period size: 47 Copynumber: 2.2 Consensus size: 51 102854672 TTTATTTTAA 102854682 ATATTTTATAT-ATATTATTTATTTTTATAAATATTATTTATACATGTAAAAT 1 ATATTTTATATAATATTATTTA-TTTTAT-AATATTATTTATACATGTAAAAT * * * ** 102854734 -TATTATATATAATATT-TTTA-TTTAT-GTATTATTTAT-CATGTTATTT 1 ATATTTTATATAATATTATTTATTTTATAATATTATTTATACATGTAAAAT 102854780 ATATTTTATATA 1 ATATTTTATATA 102854792 TTTTATATAT Statistics Matches: 50, Mismatches: 6, Indels: 9 0.77 0.09 0.14 Matches are distributed among these distances: 46 7 0.14 47 20 0.40 49 5 0.10 51 13 0.26 52 5 0.10 ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59 Consensus pattern (51 bp): ATATTTTATATAATATTATTTATTTTATAATATTATTTATACATGTAAAAT Found at i:102854793 original size:9 final size:9 Alignment explanation

Indices: 102854779--102854839 Score: 50 Period size: 10 Copynumber: 6.1 Consensus size: 9 102854769 TCATGTTATT 102854779 TATATTTTA 1 TATATTTTA 102854788 TATATTTTATA 1 TATA-TTT-TA 102854799 TATAGCTTTTA 1 TATA--TTTTA * 102854810 TTATATATTA 1 -TATATTTTA 102854820 TATATTTTA 1 TATATTTTA * 102854829 TTATATATTA 1 -TATATTTTA 102854839 T 1 T 102854840 TCCCTATATT Statistics Matches: 43, Mismatches: 4, Indels: 10 0.75 0.07 0.18 Matches are distributed among these distances: 9 13 0.30 10 15 0.35 11 8 0.19 12 7 0.16 ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62 Consensus pattern (9 bp): TATATTTTA Found at i:102854830 original size:12 final size:12 Alignment explanation

Indices: 102854785--102854837 Score: 51 Period size: 11 Copynumber: 4.8 Consensus size: 12 102854775 TATTTATATT 102854785 TTATATATTTTA 1 TTATATATTTTA ** 102854797 -TATATAGCTT- 1 TTATATATTTTA * 102854807 TTAT-TA-TATA 1 TTATATATTTTA 102854817 TTATATATTTTA 1 TTATATATTTTA 102854829 TTATATATT 1 TTATATATT 102854838 ATTCCCTATA Statistics Matches: 32, Mismatches: 5, Indels: 8 0.71 0.11 0.18 Matches are distributed among these distances: 9 1 0.03 10 6 0.19 11 13 0.41 12 12 0.38 ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62 Consensus pattern (12 bp): TTATATATTTTA Done.